Last week, Mr Duffy was cleared of all charges relating to the attack at Massereene Barracks in Antrim in March 2009 in which two soldiers were killed.
Mr McCrea said the acquittal had caused “anger and fear” in his constituency.
Responding to the comments, Mr Duffy said he was taking legal action against the police over his prosecution.
Meanwhile, Secretary of State Owen Paterson told the Commons the terrorist threat level in NI remains severe.
This means a terrorist attack is considered “highly likely”.
On the issues of the Massereene verdicts, Mr McCrea asked: “Can the secretary of state understand the anger and fear that has been felt in my constituency, and indeed throughout Northern Ireland, in light of the release of Colin Duffy, a person charged on three different occasions for the murder of innocents, yet always seems to find the get out card.
“What assurance can the secretary of state give my constituents that they are going to be safe from brutal terrorists like Colin Duffy and not be another statistic in a long line of innocent victims?”
Mr Paterson replied: “I entirely sympathise with the honourable member and his constituents’ concerns.
“We do believe in the separation of powers and this was a decision made by due process.
“I’m delighted that there was one conviction in this appalling incident… but I can assure the member that this government will bear down on all terrorists.”
MPs have parliamentary privilege when speaking during a session of the House of Commons. Mr Duffy was cleared of all charges in relation to the Massereene attack.
MaliciousResponding to Mr McCrea’s comments, Mr Duffy issued a statement through his solicitors.
It said he had instructed his solicitors to “object to the comments in the most strenuous terms and he will be making a complaint to the Committee on Standards and Privileges.”
“We are of the professional opinion that the comments represent an insult to the integrity of judicial process in this jurisdiction and serve to undermine the considered judgment of the court.
“Mr Duffy has instructed us to initiate proceedings against the PSNI and PPS in respect of his malicious prosecution and unlawful detention.”
Answering a separate question on the terrorist threat level in Northern Ireland, Mr Paterson said: “Despite overwhelming community rejection of their murderous activity, terrorist groups continue to carry out indiscriminate attacks as we saw in Londonderry last week.
“This government remains committed to countering terrorism in all its forms.”
Police believe dissident republicans were responsible for two bomb attacks in Derry last Thursday night.
The bombs exploded at the tourist centre on Foyle Street and on Strand Road, close to the DHSS office, within 10 minutes of each other
Earlier this month, a Scottish soldier found a bomb inside his car outside his girlfriend’s house in the Ligoniel area of north Belfast.
The soldier found the device while cleaning the car before going to pick up a child from school on 5 January.
Duffy believes ‘DNA planted in car’ 21 JANUARY 2012, NORTHERN IRELAND
Dissidents blamed for Derry bombs 20 JANUARY 2012, NORTHERN IRELAND
Timeline of dissident activity 20 JANUARY 2012, NORTHERN IRELAND
- Brian Shivers guilty of Massereene murders (seachranaidhe1.wordpress.com)
- Duffy says DNA was planted in getaway car (seachranaidhe1.wordpress.com)
- Twentieth anniversary of Teebane (sluggerotoole.com)
- Who Remembers Sam Marshall? The Murder Of An Irish Citizen By A Foreign State (ansionnachfionn.com)
- Shock as McCrea urges scrapping of new A6. (politics.ie)