Millwall Supporters' Club say they are "saddened" that the management of their women's team are to form a breakaway side called "London City Lionesses" and end their affiliation with the Lions.
The men's Championship club announced the news in a statement on Monday.
Millwall Lionesses - who were bottom of this year's Women's Championship - will now be run by Millwall Community Trust.
But it is not yet clear in which league they - or the new London City Lionesses - will take part in during 2019-20.
The outgoing board of Millwall Lionesses have been contacted for a response, as has the Football Association - which runs the Women's Championship.
The Lionesses almost went in to administration in April 2018 but were saved after nearly £17,500 was donated via a crowdfunding page.
"Without the generous support of Millwall fans across the country last year, stopping the club from disbanding, there would have been no club for the current regime to own," the Millwall Supporters' Club's committee said in a statement.
"We look forward to working with the Millwall Community Trust next year in a new and exciting partnership under the umbrella of Millwall FC, as it should be."
A statement on the Lions' website said: "Millwall Football Club regrets to announce that the board of directors and senior management at Millwall Lionesses have decided to become an independent entity.
"This will mean the start of a new club, London City Lionesses, while Millwall Lionesses will go on to operate through Millwall Community Trust with its proud history and tradition intact.
"The club is disappointed that the Lionesses' current hierarchy have decided to become independent. Millwall have tried several times, over the course of the season, to arrive at a different outcome.
"The club's aim, as always, is to ensure that there is a pathway for girls and women to play football at as high a level as possible and this will continue to be the case with a new-look Millwall Lionesses.
"The club wishes London City Lionesses the best of luck in the future with their new venture."