When Germany invaded Poland on September 1, 1939, Morgenstern-Podjazd sent the cadets to fight in the defense of Horodyszcze and on 19 September he had the school blown up to prevent it from falling into German hands. During the course of the campaign, Mrogenstern-Podjazd had his cadets pulled back successively to
Pińsk and then to Horodyszcze. The order to retreat to Pińsk turned out to be impractical when the Soviet Union invaded Poland on September 17, 1939. On September 23, 1939, he fled into
Hungary, where he was interned. Through he did not know it at the time, this would be the last time he was to see
Poland. On October 23, 1939, he was able to escape from Hungary into
Romania where in common with many other Polish military personnel, he was not interned by the regime of
King Carol II and instead permitted to go on to
France. After a short stay in
Bucharest, Morgenstern-Podjazd arrived in
Paris to report to the government-in-exile. In December 1939, he was appointed the first Polish naval attache to
Sweden, arriving in
Stockholm on December 17, 1939. In Sweden he engaged in intelligence-gathering about German naval activities in the Baltic. As the
Kriegsmarine normally performed its training in the Baltic while one of its main bases were located in Kiel, much of the information that Morgenstern-Podjazd forwarded to London was listed by the British as either B intelligence ("of value") or A intelligence ("of considerable value"). As the
Kriegsmarine always performed the sea trials for new U-boats in the Baltic, his information about the sea trials was especially useful for the British as it allowed them to estimate the number of new U-boats about to enter the Atlantic Ocean. During the September campaign of 1939, three Polish submarines had fled across the Baltic to Sweden where the boats and their crews were interned after the submarines stayed over the 48 hour limit. As naval attache, Morgenstern-Podjazd was deeply concerned about the Swedish treatment of the interned Polish sailors and frequently visited them to ensure that the Swedes were treating them humanely. The Swedish economy was very closely integrated into the German economy, and for much of World War Two Sweden was to lean in a pro-German neutrality as Sweden was heavily dependent upon German businesses to keep its economy functioning. Morgenstern-Podjazd spent much time taking up complaints from the Polish sailors with the Swedish government, whom he accused of violating various aspects of international law in its treatment of the interned sailors in order to curry favor with the
Reich. In the summer of 1941, a scandal broke out when Commander
Bogusław Krawczyk of the Polish submarine ORP
Wilk committed suicide on July 19, 1941. In response to the scandal, General
Władysław Sikorski, the prime minister of the government-in-exile came into conflict with Admiral
Jerzy Świrski and his deputy Commander Karol Korytowski. Sikorski had wanted to sack Admirał Świrski, but was prevented from doing so by objections from the British Royal Navy who argued that Świrski was the most experienced Polish admiral and there was no one to replace him. Morgenstern-Podjazd was appointed to replace Korytowski as Świrski's deputy. In September 1941, he flew on a British bomber to Great Britain and on September 10, 1941, took up command as Swirski's deputy. Morgenstern-Podjazd's relations with Świrski were strained and on January 23, 1942, he attempted to resign, saying he simply could not work with Świrski. His resignation was rejected by Sikorski who urged to find a way to learn how to co-operate with Świrski. On October 15, 1942, he resigned to become the Polish naval attache to the United States. He was to remain in Washington DC until June 1945. During his time in Washington, his main duty was in arranging liaison between the ships of the Polish Navy and the United States Navy assigned to the convoy duty on the "North Atlantic run" that saw merchantmen take supplies and men from North America to the United Kingdom. In September 1945, he took command of the naval training school ORP
Bałtyk in
Okehampton. In common with most of the other Polish naval officers, Morgenstern-Podjazd was greatly embittered by Poland losing its independence and saw the outcome of the war as a defeat for his country. ==In exile==