MPs have voted to reject several amendments recommended by the House of Lords on the Overseas Operations Bill.
The House of Commons voted 365 to 258, majority 107, to disagree with Lords amendment two, which was connected to the investigation process for allegations related to overseas operations.
MPs voted 357 to 268, majority 89, to reject Lords amendment four, which was connected to restrictions on time limits for actions brought against the Crown by service personnel.
MPs voted 357 to 266, majority 91, to reject Lords amendment five, which would have placed a new duty of care on the Ministry of Defence (MOD), requiring it to provide legal, pastoral and mental health support for troops involved in investigations or legal action.
A key point of contention has been the bill's presumption against prosecution for serious crimes, including genocide, torture, crimes against humanity and war crimes.
Earlier on Wednesday, the new Minister for Defence People and Veterans Leo Docherty announced all, barring war crimes, will be excluded.
He told the Commons: "Removing any more categories from the bill would unnecessarily weaken the reassurance to service personnel and veterans.
"If there is a case to answer, the prosecutor will make sure that it is answered."
Some in the chamber think war crimes should also be excluded from legal safeguards, or risk British troops facing trial at the International Criminal Court.
Conservative MP David Davis said: "War crimes is plainly in their sights.
"If somebody is guilty of a war crime, or not guilty – is alleged to be guilty of a war crime – and we exercise the presumption against prosecution, as is stated in this bill, then they will end up in front of the International Criminal Court.
"It is quite clear to me, this is not a risk, this is a certainty."
Shadow Defence Secretary John Healey told the Commons: "It is also about our adherence to, and respect for, international law. If we ourselves meet the highest standards of legal military conduct, we can hold other countries to account when their forces fall short.
"If we do otherwise, it compromises our country's proud reputation for upholding rules-based international order that Britain itself helped to construct since the days of Churchill and Atlee.
"I ask the minister and his colleagues in the MOD, to include war crimes when this bill returns to the other place".
Leo Docherty inherits a complex role – finalising a bill that is trying to protect veterans, without the unintended consequence of eroding their legal protections.