April to May
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During April 1941 it became obvious to the British staffs that there would be an invasion of Crete before long.  With the evacuation of the Allies from Greece it was now imperative that improvements be made in the defence of the island, and in the command of those forces.
On the 28th April General Wilson arrived on Crete from Egypt having been tasked by Wavell to determine together with General Weston, who at that time was in command on Crete, to make an appreciation of what was needed to hold the island.  Wavell said that the island had to be denied to the Germans, but in his view large-scale sea-borne landings would not be possible, but airborne landings were possible.  In Wilson's view Heraklion and its airfield, Canea, Suda Bay and Maleme would all have to be held at all costs.  To do this he believed it would need, as a minimum, three brigades each of four battalions, plus a motorized battalion, this was in addition to the Mobile Naval Base Defence Organization (MNBDO) which would be needed at Suda Bay.  The Greeks were also keen that their force on the island, some 11,000 men, should come under British control.  The trouble with this was that the British would need to provide them with supplies while they had enough trouble doing this for their own force, also the Greeks were poorly armed and trained.
On the 28th April the Joint Intelligence Sub-committee put out a note saying "it can be calculated that the enemy could land up to 10,000 men per day in Crete from the air, though this figure would be subject to continuous decrease in proportion to the damage and casualties inflicted on the enemy aircraft.  In addition to this scale of attack, there would be some sort of sea-borne expedition but no calculation of its size is attempted."  (WO 106/3243)  On the same day Churchill was wiring Wavell; "It seems clear from our information that a heavy airborne attack by German troops and bombers will soon be made on Crete.  Let me know what forces you have in the island and what your plans are.  It ought to be a fine opportunity for killing the parachute troops.  The island must be strongly defended."
Wavell, while expecting the Germans to attack the island, suspected that it might be a diversion; "It is just possible that plan for attack on Crete may be cover for attack on Syria or Cyprus and that real plan will only be disclosed even to own troops at last moment.  This would be consistent with German practice." (WO 106/3243)  On the 29th April General Wilson sent Wavell an overview of the disposition of the forces on the island.

"2 New Zealand battalions Maleme airfield. 4 New Zealand battalions covering western approaches to Suda.  1 Composite battalion Canea area for local protection.  1st Battn. Welch Regt. in reserve at Canea.  3 Australian battalions covering eastern approaches to Suda.  2nd Battn. Black Watch, 2nd Battn. York & Lancs Regt., 1 Australian battalion and Composite battalion Heraklion under command of 15th Infantry Brigade.  Arrangements being concerted with S.A.F.O. for obstruction of greater part of aerodromes at Maleme and Heraklion, remainder to be obstructed at time to be decided by local commanders.  Action will be taken to protect Retimo landing ground at present defended only by Greek troops.  Have little faith in value of Greek troops here but they may be useful in providing information."  (WO 106/3243)

The War Office signaled Wavell on the 29th April their appreciation of the size of the forces that might take part in the coming invasion; "available for the invasion 3000/4000 parachutists or airborne troops in first wave.  2 or 3 sorties per day possible from Greece with 3 or 4 from Rhodes.  Also 315 long range bombers, 60 twin engine fighters, 240 dive bombers and 270 single engine fighters."  Wavell agreed that the information available pointed to an invasion but once again expressed his view that "Must however bear in mind possibility cover plan Cyprus Syria and Iraq."  He was still thinking Crete might only be a diversion, and in WO 106/3243 there is a signal dated 7 May from the Military Attaché in Ankara giving a little credence to this; "Normally very reliable neutral (source) states air attack from Dodecanese on Cyprus being planned. Crete is considered too well defended." Wavell also felt that the War Office were over-estimating the enemy aircraft strength; "Consider your estimates scale air attack excessive.  Your figures appear to be based upon establishments of aircraft in Balkans, Sicily and Libya.  Our estimates based on operational aircraft likely available Balkans as follows; 150 single engine fighters, 40 twin engine fighters.  We think bulk air forces taking part would be based in Greece."  He also felt that the sea-borne invasion would have limited resources, "....insufficient sea going shipping left Aegean for large scale sea borne operation...."  His estimate of the air forces available was way out and on the 3rd May he sent an amended signal regarding these figures "add to estimate 150 long range fighters and 100 dive bombers."  (WO 106/3243)
So, although the British knew that the Germans intended an invasion, and in London they had a lot of information on this from ULTRA, they were ill prepared and had poor estimates of what was about to hit them.  Also, some had a strange idea of what could be achieved.  On the 3rd May the War Office were asking Wavell "We should be glad of your appreciation of the defence of Crete, in relation to the situation in the Middle East as a whole, in the following alternative cases;

a) Crete to be used as a re-fuelling base 

b) Crete to be denied to the enemy"

They do not say how they think Wavell might be able to hold a re-fuelling base at Suda Bay in isolation if the rest of the island has fallen.  It would seem sensible to believe that they only had option b).

Having determined that the island had to be held, and that Freyberg was to be the commander of the island forces, it was necessary to prepare the defences more adequately to repel that expected invasion, and most of the effort would go into preparing Maleme, Canea and Suda Bay as they constituted the most important area.  That said Freyberg had to hold them all or nothing, holding one area but losing the rest of the island was not a tenable option.  This area would be held principally by the 2nd New Zealand Division (Freyberg's old command) under Lt. Gen. Puttick with 5 Brigade (Brigadier Hargest) in the area of Maleme and east of the airfield, and 4 Brigade (Brigadier Inglis) in the area of Canea.  In the early phases before the battle started there would be a certain amount of movement of units between larger formations, and these units moving between different commanders.  [Davin's "Official History of New Zealand in the Second World War - Crete" is very good for keeping tabs of what was happening to the NZ units.]
The airfields were considered prime objectives of the expected attack, (code name for the attack was SCORCHER) and their holding (or obstruction and possibly destruction) was recognized, but it is worth mentioning that these were not airfields as we might think of them today; they were small, mainly earth affairs with limited tarmac and in a bad state of repair.  Air Chief Marshal Longmore had visited the island and on the 8th May his view was that the airfields were such that "casualties would be high from lack of repair facilities; and lack of cover made dispersion of aircraft difficult.  He was against the permanent stationing of squadrons but thought that the airfields might be used as advanced landing grounds for fighters." (Davin)  If, as was the case, there were effectively no RAF aircraft left on the island when the attack came (most were flying from N Africa with some landing and refueling on the island) why have the airfields.  At this point they were of more use to the Germans for landing their airborne troops (in JU52s) than they were to the Allies who had no effective air force on the island.  There was a strong argument for their destruction or effective obstruction to severely restrict any possibility of aircraft landing.  This was not done so now a large part of the island defence forces had to be devoted to defending these large airfield perimeter areas.  A crucial decision.
The photo on the right shows Maleme airfield, viewed from the north (sea) side.  Anyone driving past it today will still see that there are few buildings on the airfield.

Photo from Karlheinz Schlaweck

By the 10 May, although the main threat to the island was believed to come from the air, there were no air support forces to be spared from N Africa, this lack of air defence was to be crucial in the coming battle both for the ground and the naval forces employed.  Wavell did however recognise the part that might be played on the island by light tanks and he was to send six I tanks and fifteen light tanks.  A convoy arrived on the 14 May with the tanks which were then dispersed between the main defence areas.  But, as they approached the time for the invasion the supply situation, and its maintenance, was becoming a big concern.  It was estimated that 700 tons a day was needed to supply the defenders, and these would all need to come through the ports on the north side of the island, principally Suda and Heraklion.  Unfortunately there were insufficient AA defences around these ports to prevent the enemy aircraft wreaking a fair amount of destruction.  By the 19th May there were 13 damaged ships in Suda harbour, and a great lack of motorised transport on the island even if supplies did get through.  Freyberg's main concern at this late stage was not men on the ground, but food and ammunition, and the situation was exacerbated by the need to supply the Greek troops as well as his own.  On top of that, the presence of the Greek King on the island, with his retinue, gave Freyberg other security concerns he could have done without.  King George was taken off the island the night of the 22/23 May.

Not only were the troops and resources on the island going to have to defend the airfields, but they had to also defend the coastline.  The threat had been assessed as coming both from the air and from the sea, and in a crucial signal to Freyberg on the 13th May, giving the transcript of an ULTRA intercept, Freyberg assessed the sea-borne landing as the larger of the two threats.  As a result large stretches of beach, especially that between Canea and Maleme, had to be manned in case they were the point of invasion.  As a rsult the NZ 5th Brigade was stretched between Platanias and Maleme.  Unfortunately this meant that the open area to the west of Maleme, across the River Tavronitis was not manned due to lack of resource.  There was a Greek regiment at Kisamos Kastelli, but essentially a prime landing and form up area west of the airfield was undefended.
On the 19th May ULTRA intercepts allowed the Allies to know that SCORCHER as they called the planned invasion, or MERKUR as the Germans knew it, would begin the next day.
A later analysis of the battle drawn up by the Chief of Naval Operations in April 1943 (WO 252/1201) stated that they believed there were two alternatives open to Freyberg;

a) Partially to disperse his force with a view to protecting both the aerodromes (Maleme & Heraklion) against an airborne and the beaches in their vicinity against a seaborne attack.

b) To concentrate his force in four self-contained groups for the immediate defence of the three aerodromes and the base area at Suda. 

Freyberg adopted the first.  In order to meet the sea threat considerable dispersion was necessary west of Canea where the enemy might land at any point on the 12 miles stretch of beach.  Dispositions of the NZ Division was influenced by that factor.

They also wrote that "Perhaps the major lesson of this campaign was that to defend with a relatively small force an island as large as Crete, lying under the permanent domination of enemy fighter aircraft and out of range of our own was impossible."