Ms Mordaunt has signalled she intends to create a "statutory presumption" against prosecution of current or former personnel for alleged offences committed in the course of duty abroad more than 10 years ago.
The Ministry of Defence, however, says that would not apply to Northern Ireland, and in cases where there is compelling evidence.
"I do think it [additional protection] should cover Northern Ireland," she said during a conference at the Royal United Services Institute.
"The problem is that we have failed on the whole 'lawfare' issue because we have been waiting for other things to happen.
"This is not going to be resolved overnight. It is a priority of mine."
She went on to say: "It is a personal priority of mine that we get this resolved and we stop this chilling effect that is claiming veterans who really deserve our care."
The legislation proposals will be subject to a public consultation.
A number of ex-soldiers who served during the Troubles are already facing prosecution - a move that has angered several Conservative MPs, including former Army captain Johnny Mercer.
Video: Johnny Mercer MP says the possibility of new legislation is a 'positive first step'.
Ms Mordaunt, who is expected to unveil the new measures within days, said: "It is high time that we change the system and provide the right legal protections to make sure the decisions our service personnel take in the battlefield will not lead to repeated or unfair investigations down the line."
While welcoming the possibility of new legislation as a "positive first step", Mr Mercer said it needed to go further.
"It's a first step, it's a public consultation and we actually need to get past this and introduce legislation that is going to protect veterans from repeated and spurious investigations into what's gone on, on operation."
Mr Mercer also said his stance on not supporting the Government will continue as the "legislation has not materialised".
"Veterans being continuously pulled over to court in Northern Ireland for that conflict is something, I'm afraid, I cannot put up with."
Ms Mordaunt is also expected to reaffirm her commitment to derogating from the European Convention on Human Rights (ECHR) before the UK embarks on significant military operations.
In 2016, Theresa May announced that the government will adopt a presumption that it will take advantage of a right to suspend aspects of the ECHR at times of war.
Mrs May said at the time that the move should end an "industry of vexatious claims" which has seen veterans of Iraq and Afghanistan pursued through the courts over alleged mistreatment of combatants and prisoners over a decade after the supposed events took place.