DUP leader Peter Robinson hit out over the rioting that has marred communities in recent days, sparked by a council vote to restrict the flying of the Union flag at Belfast City Hall.
A number of people gathered in the Antrim Road area of Glengormley and outside the Alliance Party offices in east Belfast, causing traffic disruption on Thursday evening.
"People's right to protest is justified and legitimate and should be defended," Mr Robinson said.
"However, my advice is that street protests should be suspended by those responsible for organising them - in the wider interests of a peaceful society and to ensure their protests are not used by others to launch a campaign of violence."
PSNI Chief Constable Matt Baggott has already warned that police will be taking action against anyone orchestrating violence.
"The community can be assured we will be studying social media websites very carefully indeed and we will be investigating anyone who has been inciting this violence," he said.
Mr Robinson has also defended the leaflets distributed by unionist parties over the flag issue.
Those who riot and engage in violent attacks do a disservice to the flag they claim to represent. Such criminal behaviour also distracts from the real debate.
First Minister Peter Robinson
"People's right to protest is justified and legitimate and should be defended," Mr Robinson said.
"However, my advice is that street protests should be suspended by those responsible for organising them - in the wider interests of a peaceful society and to ensure their protests are not used by others to launch a campaign of violence."
Mr Robinson also defended the leaflets distributed by unionist parties over the flag issue.
"These leaflets did not call on people to come on to the streets, but asked people to engage in the democratic process," he said.
"The leaflet specifically asked people to be respectful at all times when making their views known. This is and should remain the way all such matters are dealt with in a democratic society.
"At no time did our councillors call for a picket or protest. Indeed, when others did, our councillors called for it to be peaceful - because they knew the sensitivity of the issue and the risks involved in bringing large numbers of people onto the streets."
Following the vote by Belfast City Council, the Union flag will only be flown at City Hall on 17 designated days - in line with the protocol at Stormont.
But Mr Robinson said that his party has now submitted a motion at Stormont aimed at extending the number of days the Union flag flies there.
"Sinn Féin, the SDLP and Alliance have insisted that unionists accept the outcome of the democratic vote in Belfast City Council. I trust that in that same democratic spirit, they will accept the outcome of a democratic vote at the Assembly Commission," he said.
The First Minister also called for other parties to support a unionist proposal that Belfast City Council flies a Union flag in the Garden of Remembrance all year round.
His comments come after deputy First Minister Martin McGuinness said unionist leaders must call on those involved in trouble to stop.
"This is an attack on the democratic decision taken in Belfast City Hall by those who are democratically elected to represent the people of this city," the Sinn Féin politician said.
"Political unionism needs to accept that. They need to call for an end to these protests and for those involved to step back."
Meanwhile, SDLP leader Alasdair McDonnell has slammed DUP minister Edwin Poots and Sammy Wilson for comments he deemed "reckless" in the current climate.
According to Mr McDonnell, the suggestions that the policy regarding the flying of the Union flag on designated days at Stormont needs to be re-examined could serve to heighten the existing tensions.
He said that the position at Stormont was already clear and added: "Edwin Poots and Sammy Wilson are aggravating matters by suggesting the current policy should be reviewed at a time when we need leadership and a moderate response.
"We have two DUP ministers consciously, recklessly and deliberately inflaming the situation rather than calling for calm."
There is no chance of doing something further in respect of flags at Stormont and this type of comments by two ministers only escalates the situation further.
Alasdair McDonnell, SDLP
PSNI Chief Constable Matt Baggott has said he will be meeting the leaders of Northern Ireland's political parties over the ongoing flags issue.
Speaking out over the rioting in areas including Belfast, Bangor and Carrickfergus, he said: "There can be no excuses whatsoever for intimidation and violence.
"Their actions are shameful and they put innocent people's lives at risk."
The political war of words only escalated in the wake of the violence, with the Alliance Party targeted in a number of attacks.
Alliance leader and Justice Minister David Ford has already called for the Assembly to be recalled to discuss the issue and show "united opposition" to attacks on elected representatives - a call backed by the SDLP.
"Since Monday night, we have witnessed a growing campaign of violence and intimidation against the Alliance Party - but attacks on any one political party are attacks on democracy itself," Mr Ford said.
"In Carrickfergus, we have an office destroyed, with our office in Bangor coming very close to a similar fate. We have witnessed threats made against our councillors, with the home of two hard working and dedicated North Down councillors attacked.
"All parties must come together to show that this behaviour will not be tolerated."
On Thursday evening, the First and deputy First Ministers asked the Stormont Speaker to bring forward Monday's plenary sitting of the Assembly to discuss an agreed motion on the disturbances.
Members are now expected to meet earlier than the normal midday start.
The Assembly must unite to show that an attack on our democracy will not be accepted.
David Ford, Alliance
Unionist politicians have condemned the violence, but also reacted angrily to the Alliance Party's comments.
Sammy Wilson said Mr Ford is "out of touch" with how people feel.
"Let me make something clear, a Pandora's box was opened in Belfast aided and abetted by the Alliance Party," the East Antrim MP told UTV.
"David Ford may be getting carried around in his police land rover and not be aware of how ordinary people feel, but if Alliance does not understand what was going to happen as a result of this, they are totally out of touch with people in Northern Ireland."
UUP leader Mike Nesbitt accused Alliance of using the violence to "portray themselves as victims".
He said: "It's taking the focus off what the Alliance Party has done in terms of the flag of Belfast City Hall and allowing them to portray themselves as victims.
"What they have done is demonstrate that they are not a kind of cuddly form of unionism, but they're actually anti-British in some ways and that is where the focus should be - not on the fact that they're being attacked, which is utterly wrong."