Diana Johnson, MP for Hull North and Backbencher of the Year 2018, faces losing the seat she has held for 14 years after she was "triggered for an open selection by a small number" of party members last week.
Labour members can trigger a vote if they do not want their current MP to run as their candidate in a general election.
But the rules changed in September so that only a third of local branches needed to vote to deselect a candidate for it to happen - and Ms Johnson said in her case this amounted to just 16 people.
She said: "The rules changed around reselection and this is the first clutch of MPs that are going through the rules."
Previously more than half of local Labour branches would need to vote against an MP to deselect them.
In the past the reselection process has been a formality, but some local parties have been pushing for candidates who are more closely aligned with the party’s left.
"Six of my wards - the biggest wards - have voted to reselect me."
But she said just 16 people, across the three smaller wards, had tipped the scale, which she branded a "tiny amount of people".
During a parliamentary Labour Party (PLP) meeting on Monday, Ms Johnson reportedly told colleagues one branch which voted against her had just two members present at the meeting, while one supporting her had 78 people there.
Ms Johnson said she was preparing to appeal to the party's National Executive Committee (NEC), however a Labour spokesman said: "The rules are set by party conference, not the NEC.
“Under longstanding Labour Party rules, reselection processes are held within every Labour-held constituency in between general elections. It is a core part of preparing for a election."
A Labour source told the Yorkshire Post: “The NEC doesn’t have the power to change Labour’s rules. The party’s annual conference sets the rules. Reselections have taken place ahead of every general election since 2001, apart from the 2017 snap general election.”
Labour is holding its party conference in Brighton between September 21 and 25.
But Ms Johnson said: "This is a new system, I'm going to send it off and see what they come back with, I'm certainly concerned. I think there are problems and that's why I'm going to challenge it. I don't think this is what was intended by this rule."
There was an outpouring of support for Ms Johnson when the result was announced last week.
Barnsley MP Dan Jarvis told The Yorkshire Post: “Diana Johnson is an exceptionally dedicated, experienced and capable MP for Kingston upon Hull North.
"She is devoted to her constituents and is a tireless campaigner for numerous good causes. She is hugely respected by her colleagues in Parliament.
"At a moment of national political crisis I’m sure many will question the wisdom of subjecting hard working decent Labour MPs to a distracting internal selection process.
"At this pivotal moment in our country’s history, our MPs need to be able to fully focus on the extremely important matters currently in front of us.”
Leeds West MP Rachel Reeves wrote: "You are a brilliant MP Diana and don’t deserve this. We should all be working together to get a Labour Government not trying to deselect hard-working MPs. Solidarity."
Melanie Onn, the Labour MP for nearby Great Grimsby, tweeted: "Whether it's the contaminated blood outrage or baby ashes campaign (amongst other things) Diana Johnson has never stopped fighting for her constituents or those affected in the country.