DUP leader Peter Robinson said two party senior members have received death threats.
It brings to five the number of politicians warned by police about threats since Belfast City Council voted to only fly the Union flag on designated days.
The First Minister refused to name the politicians or who made the threats, but said police had informed them their lives were in danger.
However, on Tuesday night it was confirmed that Lagan Valley MP Jeffrey Donaldson and Health Minister Edwin Poots were the senior party members warned of a death threat against them.
Said the DUP leader: “The fact is that two of my senior members have been issued with a death threat.
“The police have met with two senior members of my party to indicate that not only their lives, but the lives of their families are in danger.
“I view that very seriously and that’s why – because it’s happened to me in the past , it’s happened to many of my colleagues in the past – that I can empathise with the likes of Naomi Long who faces that kind of threat.”
Meanwhile, the leader of the PUP has called on loyalist paramilitary groups to expel members involved in recent street violence.
There have been eight days of protests over the decision to limit the number of days the union flag in flown at Belfast City Hall.
On Monday night, a police car was petrol bombed in east Belfast while a female officer was inside.
PUP leader Billy Hutchinson condemned the attack saying it had “shaken unionism”.
“If individual members are involved, then I think the loyalist organisations need to think about how they deal with that and what I’m talking about is through democratic means,” he said.
“If that is the case, I would be hoping that the loyalist leadership, if they are aware of this and have evidence that people were (involved in violence), then they would expel them from the organisations.”
It is understood the UVF leadership met in Belfast on Tuesday afternoon to discuss its position.
Police have said senior members of loyalist paramilitary groups working at local level were orchestrating violence, but said that the leaderships of those organisations may not be involved.
The attack on the police car, which was guarding Alliance Party MP Naomi Long’s east Belfast office, is being treated as attempted murder.
A number of roads in Belfast and some other parts of Northern Ireland have been blocked for short periods on Tuesday afternoon.
Northern Ireland First Minister and DUP leader Peter Robinson said all unionists wanted “the folly” of what was happening on the streets to stop, but said it would be hard to persuade those involved in violence.
“People who are so proud of the flag that they have to cover their faces I think are going to be very hard to reach,” he said.
“We’ll talk to those organisations that we know are there who may have influence on the street and a lot of them are already working to try and calm things down.
“But there is no rationale – how do you call yourself a loyalist and then throw a petrol bomb into the back of a police car, it’s absurd.”
The NI secretary of state said those involved in the recent violence were “dishonouring and shaming the flag”.
Ulster Unionist leader Mike Nesbitt has called for the protests to stop.
In the past week, as trouble flared across Northern Ireland, 29 police officers have been injured and 38 people arrested.
The latest and more serious incident took place on Monday at 19:35 GMT, when a gang of six men smashed the back window of the policewoman’s car, which was parked on the Upper Newtownards Road, and threw in a petrol bomb.
The woman escaped unhurt.
Ulster Unionist leader Mike Nesbitt said on Tuesday that violence associated with protests could not be tolerated.
“It is anti-British to attack a police officer, it is anti-British to attack an elected representative,” he said.
“Peaceful protest is fine but the chances of conducting protests without this kind of repercussion is so high that I have to ask people to give up their right.”
Ms Long, the MP for East Belfast, received a death threat last week. A police car has been stationed outside her office since then.
Condemning Monday night’s attack, Ms Long said: “There is no doubt in my mind that the car was targeted because it was undertaking patrols in the vicinity of my office and I find that absolutely repugnant.”
Assistant Chief Constable George Hamilton said: “This was a planned attempt to kill a police officer which also put the lives of the public in danger and it is fortunate there were no injuries as a result of this attack.
“I am urgently appealing to those involved in ongoing protests to listen to their political leaders and step back from protest activity before someone is seriously injured or killed.”
Asked about loyalist paramilitary involvement in the violence, he said: “Loyalism is very fragmented.”
Naomi Long MP: ”If any other MP was under a death threat… I believe the government would have intervened”
“What you have is people at a local level in some ways disconnected from the senior leadership of those organisations actively involved in violence.”