Rubuta ci gaba don wannan sakin layi - Duk da haka, a ranar 21 ga Oktoba, 1937, an kama Petlyakov tare da Tupolev da kuma dukkanin darektan TsAGI a kan zargin da aka yi na lalata, leken asiri da kuma taimakawa Jam'iyyar Fascist ta Rasha. An kashe abokan aikinsa da yawa. A cikin 1939 an canza shi daga kurkuku zuwa "sharashka" na NKVD don masu tsara jirgin sama kusa da Moscow, inda aka riga aka tura yawancin tsoffin TsAGI zuwa aiki. An ba Petlyakov aikin tsara jirgin saman yaƙi mai tsayi, wanda ya yi nasara. Duk da haka, kwarewar aiki a cikin Soviet-Finnish War
A cikin yakin basasa na 1939-1940 ya nuna cewa wannan ba shine abin da Sojojin Soviet ke buƙata ba, kuma Lavrentiy Beria, shugaban NKVD da na tsarin "sharashka", ya ba da umarnin a sake tsara jirgin saman yaƙi a matsayin mai jefa bama-bamai, tare da alƙawarin cewa za a saki Petlyakov da abokan aikinsa a kan nasarar kammala shi.