The three Labour MPs facing criminal charges over their expenses claims were suspended from the party on Monday.
Livingston MP Jim Devine and his party colleagues David Chaytor and Elliot Morley are being prosecuted on several counts of false accounting.
A Labour spokesman confirmed they had now been "administratively" suspended and would lose the whip in Parliament.
The move came as Tory leader David Cameron sought to lead Gordon Brown on the expenses issue.
The Tory leader had already withdrawn the party whip from Lord Hanningfield, who is also facing charges of false accounting.
In a speech on Monday, Mr Cameron said the prime Minister had shown he was not capable of dealing with the issues involved in reforming Parliament.
He described the decision to withdraw the whip from the three Labour MPs charged over the expenses scandal as a "humiliating" climbdown.
And he accused Mr Brown of helping to create the culture at Westminster that led to the expenses scandal and the collapse of public confidence in politics.
Mr Cameron said: "How Gordon Brown can claim to be a reformer with a straight face I just don't know."
"He can't reform the institution because he is the institution: he made it.
"The character of his Government - secretive, power-hoarding, controlling - is his character.
"Just as he's the roadblock to public service reform, he's the roadblock to political reform."
The three Labour MPs involved vowed to put forward a robust defence after their charges were detailed by Director of Public Prosecutions Keir Starmer on Friday.
They argue that they should have been dealt with by the Commons authorities rather than the police.
Mr Starmer said the MPs' lawyers had already indicated they were considering using parliamentary privilege as a defence.
On Friday, Mr Devine insisted he had not broken the law. He told STV News he was "absolutely astonished and devastated at the decision" to prosecute.
However, Commons Leader Harriet Harman insisted Monday she was "completely satisfied" that parliamentary privilege did not apply to cases like theft or fraud.
She insisted MPs were subject to criminal law in the same way as members of the public.
Livingston MP Jim Devine is alleged to have dishonestly claimed £3,240 for cleaning services and £5,505 for stationery.
Mr Morley, a former minister and the MP for Scunthorpe, is alleged to have dishonestly claimed a total of £30,428 more than he was entitled to in second home expenses.
Mr Chaytor, the Bury North MP, faces charges that he wrongly claimed more than £18,000 in rent and £1,950 for IT services.
They will appear in court on March 11 and face jail sentences of up to seven years if found guilty.
