The Cumbrians are third from bottom in the table and are still looking for their first victory of the season.
Assistant boss David Kavanagh and youth-team coach David Irons will take charge until Abbott's successor is appointed.
Abbott had been at Brunton Park since 2006, and he was appointed manager of the club two years later, but Saturday's 1-0 home reverse to Port Vale has forced the Carlisle board to act.
A statement from Carlisle read: "The board would like to go on record with their acknowledgement and appreciation of the hard work Greg Abbott has done for Carlisle United since he joined the club as first team and reserve team coach in July 2006.
"He has maintained a very professional and close working relationship with everyone at the club and he has put his heart and soul into his stated aim of bringing improvement to every level and area of the business. The trips to Wembley and the year-on-year improvement in league position, prior to last season, were testament to his efforts and dedication to the job at hand.
"This has been a very difficult period and he has worked hard to find the players he felt would help to turn things round through what has been an unbelievable run of injuries. Unfortunately the continued dip in attendances, in direct relation to results here at Brunton Park, left all parties with no other option than to reach this conclusion.
"Greg Abbott leaves Brunton Park with our utmost respect and admiration and we wish him every success for his future in the industry.
"Assistant manager Graham Kavanagh and youth team coach David Irons will oversee all first team matters until such time as a permanent appointment has been made."