Flint was speaking as Chris Leslie, seen as a potential Labour splitter, attacked his frontbench’s position on Brexit.
Leslie told the Commons “we are being played for fools by the leadership of the Labour Party”, because Corbyn is refusing to back a second referendum.
“The idea that the Labour Party is not together and arguing against this tragedy, against this disaster is for me entirely heartbreaking,” he said.
Flint said she would be “sad” to see pro-EU MPs break away, but warned that they would lose their seats.
She said: “I don’t think that will work, I don’t think that will be successful, and it will cause clearly disruption and anguish within our ranks because we’ll be losing people who I’d hope would stay.
“But they will be a minority and the truth is where are they going to stand? Because the likelihood is if they stand against Labour in our areas they will let a Tory in.
“So they won’t win, but they’ll be responsible for ensuring Tory governments.”
Flint also suggested shadow chancellor John McDonnell should not have called wartime leader Winston Churchill a “villain” in an interview with Politico’s London Playbook on Wednesday night.
She said: “I didn’t understand why he got into that, Churchill to my mind had faults and weaknesses.”
She went on: “But undoubtedly he was a massively important iconic figure and leader during our darkest time during World War Two and we should never forget.
“It’s the sum of all someone’s parts rather than the mistakes they make that we need to look at.”