Mr Marsden has levelled some serious accusations
The alleged intimidation came during a debate on the wide-ranging Anti-Terrorism Bill, Shrewsbury and Atcham member Paul Marsden said.
He claimed that MP Jim Dowd prodded him in the back, another MP resorted to swearing and name-calling and Labour Whip Gerry Sutcliffe warned him he would be attacked again if he failed to stop criticising the government.
All the accused MPs have denied Mr Marsden's allegations, which follow previous claims by him that Chief Whip Hilary Armstrong compared him to appeasers of the Nazis.
On Wednesday Mr Marsden released a statement "Labour thugs attack MP" in which he outlined his allegations.
Police warning
Both Mr Sutcliffe and Mr Dowd have described the claims as nonsense.
BBC Political Correspondent Reeta Chakrabarti said that the House of Commons is known to be a difficult place for MPs who fall out of line with their party.
Mr Marsden has said that any future repeat of the behaviour by fellow-MPs will be reported to the police.
The claims were swiftly raised in the Commons, with a call from senior Conservative MP Gerald Howarth for protection for "dissident" Labour voices.
Whips' 'intimidation'
Mr Howarth said: "I have a document headed: 'Labour Thugs Attack MP' and in this document, Mr Marsden makes a number of deeply serious allegations against other Labour Members including whips.
"He alleges both verbal and physical attacks on himself."
Mr Howarth asked Deputy Speaker Sir Michael Lord: "What action can you take to protect Members of this House from attack by other Members - particularly to protect dissident members of the government from physical attack and intimidation from their own whips?"
But Labour MP Alice Mahon said: "As somebody who has occasionally voted against the government, Mr Sutcliffe is more likely to launch a charm offensive than intimidate anybody."
Sir Michael ruled that any "complaint of the kind indicated" should be made in the normal way.