Despite helping the club gain promotion to League One last season, the 48-year-old was dismissed on Sunday night following a poor start to the current campaign.
Allen said in a statement via the League Managers Association: "It goes without saying that I am deeply disappointed to have been relieved of my managerial duties at Gillingham, having enjoyed some fantastic results in my 16 months in charge.
"Any club who achieves promotion will face challenges moving up a level so it is with regret that I have been dismissed after just six league losses this season.
"With two great wins from our last three matches as well as being four places above the relegation zone at this early stage of the season, I was extremely confident that we would meet our league targets this campaign."
Gillingham continue their campaign on Saturday when they entertain Preston North End.