MacIntyre said legal action was being taken after Kent Police had declined to retract its allegations about the programme "despite being given every opportunity to do so".
The BBC investigative reporter is suing Kent Police because he feels comments that his programme was "misleading" damaged his reputation as a journalist.
The police force has said it will contest the libel action "vigorously".
Sir David Phillips, chief constable of Kent Police, was served with a writ on Monday morning, MacIntyre announced outside the BBC's Broadcasting House in London.
The Brompton Care Home in Gillingham, Kent, was shut down by social services after an episode of MacIntyre Undercover last year unearthed what the TV reporter claimed was a "culture of neglect".
A police investigation later took place and two people were cautioned for minor assaults.
MacIntyre said legal action was being taken after Kent Police had declined to retract its allegations about the programme "despite being given every opportunity to do so".
He said: "In making these allegations, they have both damaged my personal reputation as a journalist and brought the reputation of the BBC's journalism into question."
Kent Police confirmed that the force had received a writ naming Chief Constable Sir David Phillips, Detective Sergeant Michael Costello, and the force's media services manager, Mark Pugash.
After the MacIntyre Undercover programme, which was broadcast on 16 November, four other homes were also shut down.
MacIntyre said the programme uncovered "a culture of neglect which experts in the field - as well as BBC viewers - found shocking and unacceptable".
He added: "It is a fundamental purpose of journalism to give voice to those who, because of their circumstances, are unable to speak for themselves.
"It would not serve the public interest if our findings were diminished by totally unfounded and defamatory comments made by Kent Police."
Mark Thompson, director of television at the BBC said: "The BBC fully supports this action by Donal MacIntyre."
He added: "The remarks made by Kent Police called into question a programme which revealed the abuse, humiliation and neglect of vulnerable residents."
Mr Pugash said: "We will be contesting this vigorously."