Mr Flanagan, 46, currently a deputy chief constable, was yesterday appointed as successor to Sir Hugh Annesley, who retires in November. He was chosen from a shortlist that included the RUC's other deputy chief constable, Blair Wallace, and the Commissioner of City of London police, William Taylor.
Unionist leaders immediately warned Mr Flanagan that RUC morale was low, while nationalists said the force was deeply mistrusted.
Although not well-known in Britain, Mr Flanagan has in recent years become the RUC's most familiar officer in Northern Ireland, frequently appearing on radio and television. His 26 years in the RUC have included terms in charge of its Special Branch and overall responsibility for operations.
At present, he is chairman of the "executive committee", which means he has responsibility for the direction of all police, military and MI5 activity in the province. He holds a BA in public sector studies, an MA in legal and administrative studies, and a certificate in legal administration. At 46, it is expected he will remain at the head of the RUC for many years.
He spoke yesterday of the damage done in the marching season, declaring: "Northern Ireland cannot withstand another summer like this one. The intensity of the violence which our officers withstood was of a scale that I hadn't seen over 25 years. The country stared into the face of great difficulty and crept right to the edge of the abyss It pulled back and I believe it will continue to draw back."
He said rebuilding community relations and trust was the force's top priority. He added that the RUC would be "very aggressive" in encouraging Catholics to join, promising they would find an environment in which "they don't have to submerge their religious beliefs in order to feel comfortable or in order to be successful".
Reacting to the appointment, the Ulster Unionist leader, David Trimble, said: "The poor quality of leadership in the recent past has resulted in a serious loss of morale. He would need to rebuild morale within the force."
Democratic Unionist leader, the Rev Ian Paisley, said police morale had "nose-dived" following the Drumcree stand-off. He claimed Mr Flanagan did not have the support of a majority of his officers : "He has got to prove himself. The Unionist population will be keeping a very close scrutiny on what he is doing."
Alex Atwood, of the SDLP, said the police were deeply mistrusted by nationalists, and could only establish trust by a purge of "the culture, the nature, the policies and the practices of the RUC". He said Mr Flanagan had shown evidence of edging the RUC forward but would have to take a leap forward.
Gerry Adams, Sinn Fein president, said the appointment was irrelevant, asserting that the RUC had no future and should be disbanded. "We need a police service which enjoys the confidence and support of all sections of our people. The RUC cannot achieve that."
t Large numbers of police will be on duty today when a series of Protestant parades are held across Ulster. Tension increased when the Co Armagh headquarters of the organising body, the Royal Black Preceptory, was badly damaged by a suspected arson attack.Reuse content