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Czech Lubos Kubik replaced Atkins as Torquay boss last week with new Torquay chairman Chris Roberts making instant changes both on and off the field.
Atkins was offered the chance to stay on at Plainmoor as director of football, but he has decided to move on. He told Sky Sports.com "The job isn't for me in the present situation at the club".
Torquay became Atkins's ninth club at managerial level, joining on 13 April 2006. Originally joining as caretaker manager he was then given the permanent position. He previously had spells managing Bristol R (26-04-2004 - 22-09-2005), Oxford (23-11-2001 - 21-03-2004), Carlisle (01-06-2000 - 12-07-2001), Chester (20-01-2000 - 31-05-2000), Northampton (10-01-1995 - 07-10-1999), Doncaster (01-08-1994 - 01-08-2005), Cambridge (04-12-1992 - 31-07-1993), Colchester (01-06-1990 - 30-06-1991).