In a statement, the terrorist group said that they had "executed" Mr Doherty.
The Real IRA also claimed Mr Doherty was a member of the paramilitary organisation.
The father-of-one from the Brandywell area of Derry, who lived with his partner, Mairead, and their two-and-half-year-old daughter, was due to get married in three months time.
"Kieran's partner, Mairead, and his family are traumatised and in deep shock at the sudden and brutal death of Kieran", Sinn Fein Foyle MLA Martina Anderson said on behalf of the family.
First Minister Peter Robinson and deputy First Minister Martin McGuinness said they would "stand-up" to dissidents.
Mr Robinson said: "We are going to stand up to the people who carry out these kind of activities. Where they offer fear we will offer hope."
"People can compare what we have to offer with the bloodshed and evil that other people are offering."
Mr McGuinness said of the killers: "They represent the past. We represent the future. We represent the new way forward.
"And we are absolutely dedicated and determined to stand united against the activities of these people."
Earlier Mr McGuinness had called on the 32 County Sovereignty Movement to release a statement.
"I think those people who were responsible for (Wednesday) night's dirty deed need to come forward and give an explanation to the citizens as to why they are continuing with these stupid and futile acts."
MI5
In November 2009, Mr Doherty gave an interview to the Derry Journal newspaper in which he claimed that the MI5 had tried to recruit him as an informer.
According to the paper he was trying to open a cigarette manufacturing company but had been turned down by Revenue and Customs when he was approached by an MI5 agent.
Last month, he spoke to the same newspaper to deny that he was linked in any way to the discovery of cannabis worth €500,000 in a house in Co Donegal.
Mr Doherty served a jail term in the Republic of Ireland for robbing a nightclub in Co Donegal.
Detective Chief Inspector Ian Harrison said Mr Doherty was known to police but this could never excuse his murder.
"The people who were responsible for this are criminals, they provide nothing for society, they skulk around in the dark and they are unrepresentative of this town," said Mr Harrison.
"Kieran suffered a brutal death, he sustained serious injuries. It was unjustified, it was unwarranted. These people destroyed this family's life."
He said Mr Doherty left home at about 8pm on Wednesday night and police were still trying to ascertain his movements but he may have been intending to go to a shop.
The SDLP MP for Foyle, Mark Durkan, said the killing echoed the so-called "execution" murders carried out by the IRA during the Troubles.
"I totally and absolutely condemn this brutal and crude murder which is a throwback to the very worst of our past," he said.
'How dare they?'
UTV understands Kieran Doherty was shot twice in the back of the head.
He was found by a member of the public at 10.10pm on Wednesday on the Braehead Road close to the border with Co Donegal and 400m off the main Letterkenny Road.
A priest was alerted and then the emergency services but he was dead when they arrived.
"I prayed over the man", Father Stephen McLaughlin told UTV.
"It was a chilling scene to see a human dumped along a country road in the darkness of night.
"It was cruelly ironic that it was at the rear entrance of a place of prayer, Termonbacca retreat centre."
Sinn Fein's Martina Anderson said she was "absolutely disgusted with what happened."
"The people that I have spoken to in my community, and I would say the vast majority of people across the island of Ireland, would be absolutely shocked and condemn outright what happened," she said.
"It is wrong. There is no place for this in our society. We all want the gun to be taken out of our community."
She said of the killers: "How dare they?"
Local DUP MP Gregory Campbell also condemned the shooting which "bears a remarkable similarity to murders by the Provisional IRA and others during the Troubles."
"Whilst there is much talk of stopping those responsible from dragging us back to the past, this can only be the case if the community gives whatever information they have to the police."
Detectives have appealed for anybody who saw anything, including any vehicle movements in the area at the time, to contact them.
Police across the border have been asked for help.