There have been numerous anti-war rallies
A spokesman for Prime Minister Tony Blair insisted people were free to hold their opinions, saying: "It's a democracy".
He also said Ms Armstrong had compared Labour opponents of the bombing campaign with people who tried to appease Hitler in the 1930s.
'Remember terror images'
A spokesman for Prime Minister Tony Blair said: "We have to remember why we have embarked on this action - it's all too easy to forget over time what happened on 11 September and the image of the planes flying into the towers."
With the Whips' office insisting nobody had been restricted in what they said in Parliament on the military campaign, Jack Straw attacked Mr Marsden's decision to publish a version of what had been a confidential conversation.
The foreign secretary said it was he who had first compared those opposed to military action to people who supported the policy of appeasement in the 1930s.
He said: "Of course I understand why people want to avoid that choice."
On Monday Mr Marsden again spoke out on the conflict, saying that US and UK military action was killing hundreds.
He said that opposition to the strikes within Parliament could not be assessed without a vote on the issue.
He claimed there were other Labour MPs who shared his views but who felt unable to express them.
But in an unprecedented move, Labour whip Anne McGuire went on record to suggest the media was stirring up the issue.
"I think there is a myth around that somehow the Whips' Office is this sort of dragon entity that goes round putting thumb screws on people," she told BBC Radio 4's World At One programme.
"The chief whip is entitled and is actually charged with speaking to individual members of Parliament where they have concerns over issues of policy," she continued.
"She would have been failing in her duty if she had not asked if Paul wanted to speak to her."
Ms McGuire added: "There has been absolutely no way in which anyone has been restricted in what they have been able to say in the three recalls of Parliament.
"Nobody has said that Tam Dalyell, George Galloway or Paul Marsden can't voice their opinion."
Mr Marsden is one of 14 Labour MPs who have signed a parliamentary motion calling for a halt to the military strikes.
'Hardened views'
Last week Mr Marsden claimed his critical views of coalition bombing in Afghanistan had only been hardened by party whips' attempts to pressure him into toning down his comments.
The MP has repeatedly called for a Commons vote on the issue.
At a meeting last Tuesday, Ms Armstrong urged him to follow the party line and to clear any future motions or media appearances with her, according to Mr Marsden.
Explaining that he had refused to comply with Ms Armstrong's demand, Mr Marsden said: "My views against the bombing have only hardened after this meeting."
He continued: "I made it clear that I would not be backing down on my views that Parliament should be given a vote in this war."