Chief Constable Sir Hugh Orde has accused the SDLP and Sinn Fein of insulting his staff and using the police as a political football.
Sir Hugh Orde criticised nationalist politicians
His criticism is contained in a confidential memo, obtained by the BBC.
It is understood that Sir Hugh was angered by a number of remarks by nationalist politicians.
It follows the report by the Police Ombudsman last week, which said there had been collusion between some members of Special Branch and the UVF.
The chief constable said in his memo, sent to almost 10,000 police officers last week when the report was published, that it had been "a difficult week for policing."
He again points out that he has accepted the recommendations made in Nuala O'Loan's report, which he described as "uncomfortable reading".
Sir Hugh then accuses some political parties of making "unfair and damaging statements about our organisation".
It is believed that he was angered by remarks by Sinn Fein leader Gerry Adams last week, when he said republicans would "put manners" on the police.
Sir Hugh is also believed to be annoyed by comments made by Mark Durkan in a newspaper advert last Friday.
In it, the SDLP leader claimed his party had ensured that Sir Hugh was appointed chief constable of the PSNI - to keep out what he called "the old RUC order."
In the memo, Sir Hugh said it was "unacceptable that some individuals have used policing for political purposes".
He said they had made "insulting comments about the organisation, its staff and retired colleagues", who he holds in the highest esteem.
Sir Hugh tells staff that he has spoken directly to the SDLP leadership to express his anger - and taken steps to speak to Sinn Fein, but says their leadership appears to have "gone on-the-run".
He ends his message by saying he is "proud to lead the PSNI" and says his staff "can hold their heads up high".
SDLP policing spokesman Alex Attwood told the BBC's Good Morning Ulster he was surprised by the content of Sir Hugh's memo.
"I would suggest to the police leadership that they are on the wrong side of the argument," he said.
"They need to get back on the right side of those people who, over the last five or six years, have done so much to reshape Northern Ireland society in the interests of and to the benefit of everyone."
Sinn Fein assembly member John O'Dowd rejected Sir Hugh's claim that the party had "gone to ground" when he tried to contact them.
"Sinn Fein is out there trying to introduce an accountable policing service," he said.
"And if he comes to Sinn Fein with the same attitude that he has displayed in that memo, he will be getting a short shrift answer."
Meanwhile, party president Gerry Adams is to meet the prime minister on Thursday to discuss the implications of the Ombudsman's report on collusion.