The 42-year-old former striker was appointed in April 2015 and oversaw the club’s promotion to the Championship in 2017.
Harris, who also guided Millwall to two FA Cup quarter-finals, leaves the south London side five points above the relegation zone following a seven-match winless run in the league.
David Livermore has also left his position as assistant, leaving Adam Barrett in temporary charge for Saturday’s visit of Leeds United.
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