Theresa Villiers condemned the disorder which has flared across Northern Ireland since the Union Flag was removed from Belfast City Hall, including the past six nights of rioting in east Belfast.
She said that while over 60 officers have been hurt on the front line, they are also being left open to dissident murder bids while the trouble continues.
"They are putting police in harm's way not just with bricks and petrol bombs but by opening up opportunities for attacks by dissident republicans, who relentlessly continue their attempts to murder police officers," said Ms Villiers at the University of Ulster on Wednesday.
"It is vital that this issue comes off the streets to allow local politicians and community leaders the space to sit round a table and engage in a dialogue."
The Union Flag was hoisted at City Hall on Wednesday morning to mark the Duchess of Cambridge's birthday, one of the 18 occasions during the year when it is allowed to fly under the new policy of designated days. It was lowered again in the evening.
Meanwhile UUP leader Mike Nesbitt and the DUP Lord Major of Belfast, Gavin Robinson, were among the politicians who gathered for talks at the Reverend Mervyn Gibson's Westbourne Church, as efforts to ease the unrest continue.
Clergy and community workers - and people with paramilitary connections - also attended.
If we can get the violence off the street then we need to address the underlying problems and engage the young people involved in that violence.
Rev Mervyn Gibson
It followed another night of trouble in east Belfast, during which petrol bombs, fireworks, bricks and other missiles were thrown at police by loyalist rioters on the Lower Newtownards Road. While it wasn't on the same scale as previous evening, three people were arrested and one PSNI officer was injured.
Prime Minister David Cameron said segregation between communities has contributed to the problem and challenged local politicians to break down the barriers.
In response to a question from the DUP's Nigel Dodds at Westminster, the PM said: "We need to build a shared community in Northern Ireland where we break down the barriers of segregation that have been in place for many, many years.
"I think that is part of the challenge of the tension we have seen in recent days."
Alliance MP Naomi Long welcomed Mr Cameron's comments.
She said: "I welcome the emphasis that the Prime Minister has put on a delivering a genuine shared future in the context of addressing our current difficulties.
"The violence that we have seen in recent weeks further exposes the deep sectarian tensions in our community and highlights, in my view, the lack of both leadership and commitment from many parties to delivering on reconciliation in a meaningful way."
The DUP also called for a further meeting with Mr Cameron over increasing the participation in politics of people in deprived parts of Northern Ireland.
Meanwhile Mike Nesbitt said he is disappointed that the flag was not flown from Parliament Buildings on Wednesday.
This is due to two different lists of designated days being adopted by City Hall and Stormont.
"It is a ridiculous situation that the Union flag is being flown at full mast from Belfast City Hall today, but not at Stormont, because there is more than one, agreed list of designated days," said the Strangford MLA.
"I have raised this issue with the Secretary of State's Office, and am seeking a meeting with Theresa Villiers to ask her to address this inconsistency."
Patsy McGlone of the SDLP said the longer it goes on, the more serious it gets.
He continued: "It is imperative that these protests come to an end so that, in tandem with the necessary political discussions that need to be had, businesses and economists can redouble their efforts to repair the fiscal damage caused by the destructive behaviour of rioters."
The first meeting of the new Unionist Forum, which calls for representatives to come together in a bid to end the unrest, is to take place on Thursday.
Further protests have been organised for later in the week and the weekend.