It is a decade since the council decided to fly the flag only on designated days on civic buildings in Portadown and Lurgan.
But on Monday evening, members met to discuss the flag policy and a motion was passed which will see the ten year old decision reviewed.
The motion was put forward by the DUP, and the party's MLA Stephen Moutray said previously "we did not have an understanding that Unionist family would come forward to support the motion".
Mr Moutray defended claims that all councillors had accepted the policy without complaint.
"Our party voted to oppose what was done ten years ago," he explained. "We have brought this back to the democratic forum, and that is the place to discuss it."
He said the decision to review Craigavon's flag policy was "in no way related" to the recent disorder in Belfast and added, "There have been several protests in the Craigavon and I would ask those who protest to do so in a peaceful manner."
The Alliance Party's Conrad Dixon said should the policy change, it would be "rewarding those who have engaged in violence and intimidation".
This will not only destroy good will among local communities, but has rewarded those determined to drag our society back into sectarian trenches.
Cllr Conrad Dixon
"I would question the political motives behind the decision of my DUP colleagues in bringing this motion to the Council," added Cllr Dixon.
Sinn Féin councillor Johnny McGibbon said the upcoming review must be an honest one.
"For the past 10 years, since 2002, Craigavon Council has operated a designated days policy agreed by all parties, and a genuine review could conceivably propose the removal of all flags from public buildings," he explained.
"The DUP are raising this issue in response to death threats against and attacks on elected representatives, attacks, including a murder attempt, on the police, and illegal protests and the blocking of roads. In reality they are providing weak leadership," he added.
The motion follows a decision taken in December by Belfast City Council to limit the number of days when the Union flag is flown from council-owned buildings from 365 days to 18.
Despite opposition from unionist councillors, the SDLP and Alliance Party voted for the reduction.
Violence sparked across Northern Ireland, including five consecutive nights of disorder in east Belfast this month.
A number of police officers have been injured during the disorder, and elected representatives, including Alliance MP and, most recently, SDLP MLA Patsy McGlone have been the subject of threats and attacks.