During World War II Harlinghausen was the leading exponent of anti-ship warfare with the destruction of 22 ships credited to him.

In 1936 he was selected to command an anti-shipping unit in the Condor Legion and subsequently served in the Spanish Civil War.

Harlinghausen was simultaneously appointed Geschwaderkommodore of Kampfgeschwader 26 and Bevollmächtigter for das Lufttorpedowesen (Plenipotentiary for airborne torpedoes).

[8] In January 1938, Harlinghausen, then ranked as Hauptmann (Captain) took command of AS/88 (Seefliegerstaffel—sea flying squadron), an anti-shipping unit in the Condor Legion.

The high command remained aloof from naval air power matters because it did not foresee a war with the British Empire.

[32] In a memorandum, dated 15 January 1940, the navy wished to procure the Dornier Do 217 bomber, then under development, but Hermann Göring, commander-in-chief of the Luftwaffe, refused citing the intent to transfer all offensive operations over to Fliegerkorps X, along with all new types.

[39] On 1 March 1940, a He 111 from the Korpsführungkette (Corps Command Section)/Fliegerkorps X with Harlinghausen aboard, sank the 1,388 grt Norwegian freighter, Vestfoss south-east of Copinsay Island.

[39] On 20 March he sank the transport Barn Hill (5,439 grt) on a southward armed reconnaissance mission into the English Channel.

[44] The Luftwaffe order of battle April 1940 included transport groups KGr zbv 101–108, equipped with the Junkers Ju 52.

Admiral Charles Forbes kept his distance from the Norwegian coast after a series of damaging air attacks on his Home Fleet.

[52] Harlinghausen's air corps flew in supplies to Eduard Dietl in the days following the invasion, as his forces fought the Battles of Narvik.

His reconnaissance mission guided 3./StG 1 to the area and the Junkers Ju 87 Stukas sank the anti-submarine warfare trawlers Siretoko, Jardine and Warwickshire.

[55][56] Harlinghausen's command made a significant operational contribution to the German victory in the Norwegian Campaign by rendering Allied sea communications insecure.

Interdicting shipping lanes, air superiority and transport operations were crucial to the eventual German victory.

[citation needed] The air corps sat out the Battle of Britain until mid-August 1940, while Luftlfotte 2 and 3 carried out the main effort in southern Englanḍ.

The operation was a failure and the air corps suffered heavy losses among bombers and long range fighter escorts.

The bomber approached on the beam at low-level and released bombs to damage the ship's hull below the water line.

It formed the first wave of attacks on the intensively bombed British base at Malta and to support the Axis powers in the Battle of the Mediterranean.

[66] Even with two antishipping experts occupying the position of commander, and chief of staff, the air corps failed to neutralise or paralyse the island's defences.

The staff blamed limited supplies and the distractions on other fronts for the failure to achieve more; and above all, closing the Strait of Sicily to British naval forces.

In one case, a sustained attack upon convoy OB 290 on 26 February 1941 accounted for seven to nine vessels (49,865 GRT), all sunk by KG 40 Fw 200s.

Soon, British CAM ship (catapult aircraft merchantmen) appeared, and the time of light Condor losses ended.

[73][76] Three months into his leadership, Harlinghausen was held responsible for the Luftwaffe's failure to prevent the loss of the battleship Bismarck, which sank on 27 May 1941.

[80] Harlinghausen's insistence on flying combat operations left his command leaderless after he was shot down and wounded without his usual pilot Robert Kowaleski on 13 October while attacking a transport ship in the Irish Sea.

I and III./KG 26 were ready for operations and deployed to Norway[83] while II./KG 26 transferred to the Eastern Front in April, only to return in early August.

Southwest of the Scilly Isles on 3 and 4 August it carried out its first torpedo attack against a small convoy and claimed six ships totalling 20,000 grt.

The Second Battle of El Alamein destroyed their foothold in Egypt and led to their pursuit across Libya by the British; Operation Torch had seized Algeria, Morocco and threatened to take Tunisia.

In contrast, Harlinghausen ordered his anti shipping units to abandon forward bases in Sardinia for the mainland, due to Allied air raids.

In April and first week of May, 1943, 177 Junkers Ju 52s were lost; six months after the beginning of the failed air lift during the Battle of Stalingrad.

[103] After his dismissal, Harlinghausen briefly returned to Fliegerführer Atlantik as a member of Kessler's staff but was placed in reserve on 26 June 1943.