With the outbreak of war, hostility towards Perrot in Scrignac grew, as he was suspected of pro-German sympathies. On 16 October 1939 telegraphic lines in the region of Huelgoat were cut. Perrot was accused by authorities of sabotage. The gendarmes searched his estate twice and interrogated him, but he was released as he had an alibi. However, one gendarme publicly accused him of cutting the wires, and Perrot accused the gendarme of defamation. Afterwards, an enquiry established that a military prisoner was responsible for cutting the wires. At the request of the colonel of the Gendarmie of Quimper, the abbé dropped his accusation of defamation. During the war, he continued to produce "Feiz ha Breiz". Braving the ban by Adolphe Duparc on celebrating nationalist anniversaries during the occupation, he organised the members of Bleun-Brug in Tréguier on the 29 and 30 August to celebrate the 500th anniversary of the death of Duke Jean V of Brittany. In October 1942, he was named a member of the Comité Consultatif de Bretagne (CCB), a non-elected council put in place by Regional Prefect Jean Quénette to put forward proposals relating to Breton language and culture. In July 1941, Perrot took part in the German-sponsored effort to unify the writing of Breton. Perrot sympathised strongly with the collaborationist Breton National Party. When his parsonage was partly requisitioned by the Germans, Perrot was accused of assisting them. According to Henri Fréville, on 7 August 1943 Perrot was questioned about the movements of members of Bagadou Stourm, Breton nationalist stormtroopers allied to the Nazis, who had stopped at Scrignac. He was hospitable toward the Bagadou Stourm Youth, who were most active around Finistère, where leaders such as Yann Goulet and L’Haridon had been arrested by the French police but released by the Germans. On 12 December 1943 the abbé was killed by Jean Thépaut, a member of the French Communist Party following a series of denunciations of Perrot for alleged collaborationist activity. After his death, the collaborator Célestin Lainé recruited about sixty men whom he organised under the name "Bezen Kadoudal". Ael Péresse, second-in-command to Laîné, suggested naming the group after Perrot, so it became Bezen Perrot instead.