Saifi, 27, a native of Shaheen Bagh in Delhi, was arrested by the Anti-Terrorism Squad (ATS) of Maharashtra police and Central Intelligence after the train arson attack case.
Earlier on Thursday, NIA had conducted searches at 10 locations in the national capital in connection with the attack case that took place on April 2 this year. The agency sleuths carried out raids at Delhi's Shahin Bagh and other locations of suspects.
"Last night we received input from the Intelligence Agency that the suspect in the Kerala case is likely to be in Ratnagiri. Based on the information, we took out a joint operation with Ratnagiri police to trace the accused," the officer said.
The accused, identified as Shahrukh Saifi was nabbed from Maharashtra's Ratnagiri district on Tuesday night based on a sketch released by the Kerala Police.