[2] In 1939, after the Japanese conquest of Nanjing, Zanin remained in occupied territory,[3] delegating to an American Franciscan his authority regarding the area held by the Chinese government, whose provisional capital was Chongqing.

On the other hand, after the killing, near a mission headquarters, of Chinese soldiers under Japanese command, some 60 Catholics, including a bishop, thought to have been involved were arrested with the intention of subjecting them to court-martial, but after intervention by the French diplomatic representatives were, except for one priest, released on condition that the bishop, who had previously refused to meet the Japanese authorities, be removed from his post.

[6] Zanin mandated strict neutrality, asking the bishops to tell their priests "to avoid even the appearance of any action that ... could give an excuse for retribution against the mission residences.

"[4] This was unpopular with those who advocated some form of passive or active resistance to the invader,[7] and led to formal representations from Chiang Kai-shek's government.

[8] Claude Bowers, the American ambassador in Chile, described Zanin in the late 1940s as "a tall, slender man with graying hair, ... highly cultivated, exceptionally able and brilliant".