The Whites have started the season slowly and are second from bottom of the National League.
Dover just missed out on the play-offs last year having got in the season before.
The 64-year-old has been in charge since 2013, his second spell at the helm.
But chairman Jim Parmenter says he couldn’t allow their struggle to continue and confirmed he took action.
Parmenter said: “This has been a really tough decision to take, I have worked with Chris for a long time, he has been highly successful with us, but football is changing.
“There has clearly been some poor player recruitment decisions taken during closed season, which is something we will be addressing.
“There are also a number of issues around training and our ways of working, which we will be looking at.
“We have a good setup at the club, a decent playing budget and supporters who want to be proud of their team.
“We need to move forward in a manner that gives us the best opportunity to progress – that means avoiding relegation as a minimum and ideally pushing on towards the other end of the table.”