The Defence Secretary Ben Wallace has described the conflicts in Iraq and Afghanistan as "illegal wars".
Mr Wallace made the remarks in the Commons during the second reading of the Overseas Operations (Service Personnel and Veterans) Bill.
In a heated exchange with John Healey, shadow defence secretary, Mr Wallace said: "Much of the mess we are having to come and clean up today is because of your illegal wars, your events in the past and the way you have run the safety of our forces."
The legislation has been warmly welcomed by Iraq war veterans after thousands of troops remained under investigation many years after the invasion of Iraq in 2003, a military campaign executed under former Labour Prime Minister Tony Blair.
All of those cases, excluding one, have since been dropped due to a lack of evidence while the lawyer, Phil Shiner, who brought the cases was struck off for dishonesty.
Almost 3,500 criminal allegations - including murder and torture - were filed against soldiers serving in Iraq.
Mr Healey told the Commons that the Bill failed to protect troops from prosecution on historical matters and accused the Government of bringing in a "legal presumption against prosecution for torture, war crimes, for crimes against humanity".
Mr Wallace added that Mr Healey’s comments were “a disservice to our troops and is all about making an excuse for not supporting the Bill”.
However Mr Healey accused the Defence Secretary of playing “party politics” and said such games “should be beneath the Secretary of State”.
“We on the Labour Benches will work with the Government to get the Bill right,” he said.
The Government believes the new legislation will ensure service personnel will be protected from "vexatious claims and endless investigations".
It seeks to limit false and historical allegations arising from overseas operations by introducing a statutory presumption against prosecution, making it exceptional for personnel to be prosecuted five years or more after an incident.
To override the presumption, the consent of the Attorney General will be required, and the prosecutor must weigh up the "adverse impact of overseas operations on service personnel" and, where there has been no compelling new evidence, the public interest in cases coming to a "timely conclusion".
But campaigners and some senior military figures have warned that the legislation will create a presumption against prosecution of torture and other serious crimes, except rape and sexual violence. Mr Wallace rejected claims that the Bill could decriminalise torture and murder.
"We've been told that this Bill is controversial. Some have gone as far to have said it decriminalises torture or prevents veterans from receiving compensation,” he said.
"Both allegations are untrue. I have to question if those making those points have actually read the Bill in full."
Mr Wallace added that in future the Government wanted to “allow soldiers to focus on the danger and job in hand when in operations, not on whether they will have a lawsuit slapped on them when they get home”.
MPs approved the Bill at second reading by 331 votes to 77, majority 254.
Three Labour parliamentary private secretaries resigned from their positions to vote against the Bill, in defiance of the party's instruction for MPs to abstain.
Beth Winter, Nadia Whittome and Olivia Blake are understood to have been warned if they voted against the Bill they would be resigning their roles.
They were joined by 15 other rebels on the party's left-wing who voted against the legislation, among them Jeremy Corbyn, John McDonnell and Diane Abbott.