Labour's shadow chancellor wants a free vote on Syria air strikes, saying the issue is "above party politics".
John McDonnell said MPs should be able to make their "own judgement".
Asked about a possible Commons vote to decide the issue, he told the BBC: "There are some issues like going to war that should be above party politics."
John McDonnell wants a free vote on bombing Syria, which Jeremy Corbyn is opposed to
Labour leader Jeremy Corbyn is opposed to air strikes in Syria against Islamic State (IS) militants. He revealed his continued opposition to his party in a letter on Thursday, which triggered suggestions there would be a power struggle at the top of the party and even resignations. Since then he has again written to his MPs asking for their views on bombing Syria.
On Thursday Prime Minister David Cameron urged action on Syria saying: "The threats to our interests and to our people are such that we cannot afford to stand aside and not to act."
Cameron went on to say that IS was "not a threat that can be negotiated away".
The BBC reports that senior ministers are expected to phone Labour MPs over the weekend urging them to back Cameron's plan to join the air strikes. The broadcaster reported that the foreign secretary, the defence secretary and the governments' national security adviser will make the calls.
McDonnell said the "horrendous mistake" of the Iraq war had been partly due to MPs being "whipped and threatened and pushed" into supporting "something many of them did not believe in".
Speaking on BBC Radio 4's Any Questions, he said: "I think we are moving to a situation where hopefully in all parties on issues like this a moral conscience should be above the whip as well.
"On certain issues, the ones really above party politics, we have got to have mature politics in our democracy now. This is a matter of conscience. You are sending people out possibly to die.
"There shouldn't be any party discipline on matters like this. You should follow your own judgement on what you think is best for the constituency and the country."