The first P-1s and P-2s were delivered to 2./Aufklärungsgruppe in 1940, and were used over Britain. Flying at up to 41,000ft they were immune to interception at this date, and would remain very difficult to intercept over Britain at all times.
During 1941 the Ju 86P was used by 4./Aufkl.Gr.33, an experimental unit which operated them over Britain as well as over the Soviet Union in the period before the German invasion. After the start of Operation Barbarossa the reconnaissance groups moved to the eastern front, where once again they were immune to interception.
This immunity would disappear in the skies over North Africa. In May 1942 a number of P-2s were issued to 2.(F)/123 (or Auflk.Gr.23), based at Kastelli on Crete. From Crete the P-2s were able to reach Egypt and North Africa, where at first they were still safe.
On 24 August 1942 a specially modified Spitfire V, taking advantage of the more favourable atmospheric conditions in North Africa, intercepted and shot down the first Ju 86P to be lost to enemy action at 12,800m (42,000ft), in the skies over Cairo. This loss triggered the introduction of the rear firing machine gun, but over the next few days two more Ju 86Ps were lost over Aboukir, and the high altitude reconnaissance flights came to an end.
In the following month the first interceptions were made over Britain. Although no Ju 86Ps were lost it was clear that their period of immunity was over. Daytime reconnaissance flights stopped then, and in May 1943 the type was withdrawn.