Gillingham chairman Paul Scally accepted the resignation of manager Ronnie Jepson because he believed it was in the club's best interests.
Former Burnley coach Jepson offered his resignation this morning following the 3-0 defeat against Southend yesterday.
The loss at Roots Hall was Gillingham's fifth in their opening six matches of the season and leaves the Kent club in 22nd place in League One.
Scally told Sky Sports News: 'It just wasn't happening. A change was necessary and it was in the best interests of the club that he resigned.
'I did not want to be in this position but we are in a results business and we can not have another season like last year.
'We have had problems with the team and he has not addressed those problems and dealt with the team. It is not a decision that has been made on one result it is more down to the way we have been playing.
'We have a talented squad and we believed we could have a good season - we still believe it could be. But for whatever reason Ronnie could not get them playing to the level they could be.'
Jepson had been in charge at the Priestfield since November 2005 when he replaced Neale Cooper as manager, initially on a caretaker basis.
The Gills finished 14th and 16th in League One during his two years in charge.
Last weekend's 2-1 home win over newly-promoted Walsall is Gillingham's only success this season to date.