Northern Ireland Secretary Theresa Villiers told the Commons there was nothing British about the "thuggish, lawless and despicable" behaviour that also saw a murder bid on a police woman and a death threat issued to East Belfast Alliance MP Naomi Long.
The Democratic Unionist Party said police have informed two of its senior elected representatives, and their family members, they have also been subject to death threats - though it is unclear whether they emanated from loyalists or republicans.
Disorder has broken out at loyalist protests organised against last week's vote by Belfast City Council to reduce the number of days the Union flag flies over City Hall. Thirty-two police officers have been hurt and almost 40 people have been arrested in eight days of violence.
"No one can be in any doubt about this Government's support for the Union and its flag, but those people engaged in the kind of violence we have seen in the past few days are not defending the Union flag," said Mrs Villiers. "There is nothing remotely British about what they are doing; they are dishonouring and shaming the flag of our country with their lawless and violent activities. They discredit the cause they claim to support."
She added: "There can be absolutely no excuse or justification for the kind of thuggishness and lawless behaviour; it is despicable, we condemn it unreservedly and it must stop immediately."
Despite calls from Westminster and across the political divide in Northern Ireland for an end to the demonstrations, fresh pickets were held in the south and north of the city.
Representatives of all unionist parties and independents in the Assembly met to discuss the fallout of the removal of the Union flag from Belfast City Hall. They discussed a consultation process regarding the flying of the flag from Parliament Buildings, Stormont. In attendance were First Minister and DUP leader Peter Robinson, leader of the Ulster Unionist Party Mike Nesbitt, leader of the Traditional Unionist Voice Jim Allister, Ukip representative David McNarry and Independent David McClarty MLA.
Ireland's deputy prime minister, Tanaiste Eamon Gilmore, strongly condemned the return of violence to the streets of Belfast. He called for an immediate end to the intimidation of public representatives, in particular those of the Alliance Party and their families. He also condemned Monday night's petrol bomb attack on a female member of the Police Service of Northern Ireland, and described the recent wave of violence as "an attack on democracy itself that has no place in the politics of this island".
An 18-year-old man was arrested and charged with obstructing a highway. It followed a protest on the Crumlin Road in north Belfast on Tuesday evening. Police are also appealing for information about an attempted hijacking of a car at a protest in Londonderry. The occupants of the vehicle were left shaken but unhurt.