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Peter Taylor quit the Gills because his role as director of football was no longer viable.
Taylor met with Gills chairman Paul Scally on Thursday morning and announced his decision to resign.
Mr Scally put Taylor in temporary charge of the Gills following Ady Pennock’s departure, but the only win came in the Checkatrade Trophy.
After leaving the club, Taylor said: “I wanted to carry on (as interim boss), not long-term, but I felt I could have helped.
“I felt I could have contributed to helping the team.
"I said to the chairman I would like to carry on. He didn’t think it was a good idea and the people he is thinking about bringing in (as permanent manager) meant my role (as director of football) would change.”
Taylor had originally come in this summer to help head coach Ady Pennock.
“I came in to help a young manager,” said Taylor.
“I respect the chairman’s opinion and his decision. He has to make these big decisions.
“I felt my role was going to be changing and I wouldn’t have been doing the same things as what I came in here to do. In the end I felt that the role I came in for wouldn’t be there anymore and it wouldn’t have been right to stay on.”
When asked if his exit means a new manager is imminent, he said: “I don’t know, I can’t comment on that.”
Despite results not going for the Gills, Taylor was enjoying his third spell at the club.
“I definitely enjoyed it,” he said.
“I enjoyed looking after the team and I was happy to carry on. I felt that my experience would help.
“If another director of football role or a coaching position came up, or whatever, then I would up for it 100%. I wanted to carry on at Gillingham, I was enjoying it.
“Hopefully they (Gillingham) can get someone in and start getting some wins.”
A brief club statement, released following Taylor's exit, said: "Peter was appointed to work alongside Ady Pennock, however given that Ady has now left the club, Peter has also decided there is no role for him going forward.
"First-Team Coach Steve Lovell will continue to manage the team, assisted by the club's coaching staff."