Nikishov was born in 1894 the son of a peasant in Varkino, in the Saratov Governorate of the Russian Empire (now Volgograd Oblast). He joined the Communist Party in 1919. He entered a career in the NKVD and became its head for Azerbaijan in 1937, where he directed the purges. In 1938 and 1939 he was the head of the NKVD at Khabarovsk.
In 1940 Nikishov was appointed director of the Dalstroy organization. At Magadan he divorced his wife and married the commandant of the women's camp, Alexandra Gridassova (rus.). The couple established a life of luxury in the Siberian wilderness replete with servants, cooks, chauffeurs, and a cultural brigade for entertainment. Nikishov increased the gold production from the Kolyma mines. His difficulties in securing supplies for his operation were solved when the Lend-Lease program went into effect; he could divert cargo delivered to Magadan for services in the Gulag. Ships of the Dalstroy fleet were sent to the United States for overhaul and repair for their duty to transport prisoners to the Gulag. In 1944, Nikishov and NKVD general Goglidze were successful in presenting to the impressionable Henry A. Wallace, the American Vice President, a sanitized version of the Dalstroy enterprise. On 20 January 1944, he was awarded the title Hero of Socialist Labour for increasing the production of raw materials in Dalstroy.
Nikishov was a candidate member of the Central Committee of the Communist Party of the Soviet Union from 1939 to 1952.
- Blum, John Morton (1959). Years of Crisis, 1928–1938. From the Morgenthau Diaries. 1. Houghton Mifflin.
- Bollinger, Martin J. (2003). Stalin's Slave Ships: Kolyma, the Gulag Fleet, and the Role of the West. Praeger. ISBN 9780275981006.
- Tzouliadis, Tim (2008). The Forsaken. Penguin. ISBN 978-1-59420-168-4.