Terry Spence made the comments at the organisation's 41st annual conference at the La Mon Hotel.
"We are not cannon fodder," he told invited guests and delegates from police representative bodies from throughout Britain, Ireland and northern Europe.
He was referring to weeks of sporadic rioting which broke out after the decision of councillors at Belfast City Hall in December to only fly the Union Flag on designated days, during which numerous police officers were injured.
"Much of our initial difficulty and injuries can be attributed to us slavishly following the Association of Chief Police Officers' guidelines on tactics to be deployed in the use of baton rounds in public order confrontations.
"To put it bluntly, we were policing public order in Northern Ireland according to guidelines more appropriate for the rest of the United Kingdom," he explained.
What is needed to subdue or prevent public confrontation is the early and rapid deployment of AEP baton rounds. The sight of AEPs tends to concentrate the minds of potential rioters.
Terry Spence, Police Federation of NI
"Their early use keeps rioters at sufficient distance to prevent an array of sometimes deadly missiles bombarding officers from every direction."
Mr Spence continued, saying that too often it is "fear of adverse comment from our politicians" that inhibits senior officers from fulfilling their duty of care to the men and women on the ground.
"Unless our approach to dealing with public confrontation is understood to be robust from the beginning then the cost of holding the line during the frequent breakdowns in normal politics in Northern Ireland will always be paid by ordinary police officers. "
He highlighted that there was a continued public order threat from loyalist paramilitaries and the East Belfast UVF in particular.
"This protest is a sad reflection of two problems now deeply rooted in our society - the lack of progress in community relations and the economic reality facing young people, who do not stay in education or cannot find jobs."
Since July 2012, there have been over 448 officers injured as a result of public order, he said.
"Since December, 136 officers have been injured specifically as a result of the flag protest.
"It also seems to be a matter of misplaced pride that we have upheld the human rights of loyalists, egged on by elected politicians, many of them occupying senior party positions, to protest on the streets against what was clearly a democratically taken decision by Belfast City Council."
Mr Spence said that his Federation has "a different perspective on what we ought to take pride in."
"And it's certainly not the pretence that protestors have the right to disrupt the working, social and business life of the rest of the population.
"My colleagues in the frontline would also dispute what the PSNI appears to believe constitutes a serious injury.
"Being struck with iron bars, axes and concrete slabs so that limbs are broken or severely bruised. Noses broken, because visors are being smashed into faces. Shoulders dislocated so that an officer may be on sick leave for months are nothing less than serious injuries.
"Injuries are also frequently accompanied by post traumatic stress disorder and that cannot be dismissed as anything less than potentially serious."
Social deprivation is fertile ground for paramilitaries.
Terry Spence, Police Federation of NI
Discussing the Good Friday agreement, he said that while Northern Ireland is a safer place to live, the region has "not progressed as much as we would like to pretend when we go looking for foreign inward investment and tourists."
"In many respects our community relations have not progressed at all.
"Wave a flag and our society, from its most senior ministers to our most socially and materially deprived people can find common cause. All pretensions to a new and brighter Northern Ireland go out the window as they reveal a mindset unable to move beyond 1690 or 1916."
Highlighting the severe threat from the dissident republican paramilitaries, he described them as a sad group of misfits, "who cannot accept that violence in pursuit of any political objective, has no place in a democracy."
"Since January we have had 16 shooting incidents and 33 bombing incidents," he continued.
"The proposal by the Home Secretary that conviction for the murder of a police or prison officer should result in a whole life tariff, something we as a Federation have called for in the recent past, would be warmly welcomed by my members here in Northern Ireland
"I would also suggest that members of the judiciary should also be included within the scope of the legislation. There is no other place in the United Kingdom where public servants are routinely targeted for murder as custodians of the law. This is a change in the law which could bring some sobering focus to young terrorists," he added.
"We have major concerns about the coming together of these disparate groups, together with their increasing sophistication and utter disregard for the risk of incidental casualties.
"Paramilitary beatings and assaults, have resulted in serious and in most cases permanent injury to 36 civilians. Nine have been shot in what passes for justice among the terrorists.
"Despite the level of active threat, the PSNI, through pro active policing, have been able to make significant arrests. Working closely with An Garda Siochana in the past year we have arrested over 157 suspected terrorists and have brought 50 before the courts."
Mr Spence also voiced his concern over the number of young people, who have appeared before the courts in relation to terrorism.
He said they would hardly have been old enough to be at school at any time during the Troubles.