Last week the government published a series of amendments, including a requirement for the attorney general to provide consent for any serious prosecutions.
The government said its amendments “significantly reduce” the prospect of military veterans facing “rinse and repeat” investigations.
But the secretary of state rejected claims the changes amounted to an “amnesty” for former soldiers.
While some have argued protections for veterans do not go far enough, Sinn Féin has branded the amendments a “veterans’ charter”.
The Democratic Unionist Party (DUP) has also raised concerns that MPs have not been given enough time to scrutinise the changes.
Speaking in the Commons on Tuesday, Sir Chris said the bill was seeking to achieve a “balance” in its provisions.
“This bill isn’t about one group or another,” he told MPs towards the conclusion of several hours of debate.
“It’s not about special favours for one group or another.”
A spokesperson for the Irish Department of Foreign Affairs said the amendments on the bill marked an “important milestone”.
“Last year’s joint framework was a momentous step forward, and what is needed now is full and timely implementation,” they said.
The Foreign Affairs Minister, Helen McEntee, had been in close contact with the NI secretary over the past number of weeks, the statement continued.
“It is vital that implementing legislation is compliant with the ECHR [European Court of Human Rights] and faithful to the joint framework, so that it can deliver for victims and their families.
