Harris, the club’s all-time top goalscorer, succeeded the sacked Ian Holloway in March but could not prevent the south London club being relegated from the Sky Bet Championship.
Despite a run of just three defeats from nine games, Millwall’s fate was sealed on Tuesday with Rotherham’s victory over Reading, and they will join Wigan and Blackpool in League One next season.
Nevertheless, Lions chairman John Berylson insists he has been impressed with Harris’ and new assistant David Livermore’s impact on the team.
Berylson said: “When Neil took over we were already in a very difficult position.
“The fact that we came so close to taking the season to the last game says a great deal about the job that he and David have done over the past few weeks.
“I have been greatly impressed with the professionalism and attention to detail Neil has demonstrated since becoming manager and he has undoubtedly inspired the players to produce some performances of real character.
“After five seasons in the Championship, relegation is undoubtedly a massive disappointment to us all. However, we started re-structuring back in February with the addition of a head of recruitment.
“Coupled with our flourishing academy, which under Scott Fitzgerald has begun to produce good young players, there is a real sense of optimism going forward.
“I am fully committed to the future and know that our team is in the hands of men well versed in what it takes to make a successful Millwall side.”
Harris’ first spell as a player for Millwall between 1998 and 2004 bore 98 goals in 268 appearances before he added a further 40 in 162 games between 2007 and 2011.
Assistant Livermore also played with Harris at Milwall during a spell that lasted between 1999 and 2006 and previously managed non-league Histon.