The 55-year-old took over from Dusan Bajevic in December but, despite initial positive results, the Athens club have suffered three defeats in their last four matches which has damaged their bid for a European place.
Atromitos' latest loss came on Saturday at home to struggling Aris Salonica.
"Atromitos FC technical director Giannis Angelopoulos met today with coach Nikos Anastopoulos to discuss the progress of our team the last few games and it was jointly decided to end our cooperation," the club said in a statement.
Local media reports said former Olympiakos Piraeus and PAS Yiannina goalkeeper Dimitris Eleftheropoulos and former AEK Athens and Asteras Tripolis boss Nikos Kostenoglou were two leading candidate for the vacant job.
Atromitos are fourth in the 16-team Super League table with two games to play after collecting 42 points from 28 matches.
- Sports & Recreation
- Atromitos FC
- Nikos Anastopoulos