Undercover officers from Scotland Yard were present at a protest relating to a murder in Northern Ireland, a lawyer said.
The London Metropolitan Police has contacted the family of at least one victim to inform them.
It planned to notify another family for a similar reason, the Police Service of Northern Ireland disclosed in legal documents revealed in court.
Campaigners have won a full hearing into the failure to include Northern Ireland in a public inquiry announced by then-home secretary Theresa May in March 2015 under the leadership of Sir Christopher Pitchford.
It follows revelations about the activities of undercover officer Mark Kennedy, who admitted having "intimate relationships with a number of people while undercover".
Ben Emmerson QC told Belfast's High Court: "Chief constable has advised that the Met has contacted the family of at least one murder victim in Northern Ireland to inform them that officers were present at protest activity relating to the murder and that the Met plans to contact another family for a similar reason."
He added: "There is sufficient connection to two murders in Northern Ireland for there to be a need to notify the families of the involvement of undercover officers."
Stormont Justice Minister Claire Sugden this summer wrote that the PSNI was now aware that officers from the Met's disbanded Special Demonstration Squad and the National Public Order Intelligence Unit were known to have used Northern Ireland as a result of their infiltration of protest groups, the barrister said.
It followed a review by police of thousands of documents.
Mr Emmerson said: "We now know that there was an extensive operation taking place in Northern Ireland without any supervision at all."
He said the same officers operating in England and Wales had continued their activities in Northern Ireland, adding, "this is about secret police officers from London infiltrating groups without the knowledge of PSNI".
He said there was a public interest in his case and the Home Office and Northern Ireland Office had failed to give adequate reasons for their decision not to expand the remit of the Pitchford Inquiry.
He outlined an allegation that undercover officers had encouraged the commissioning of serious crime and then given evidence in their false identities, committing perjury in court and resulting in wrongful convictions.
"This is is serious stuff," he said. "We simply don't know whether there may be individuals serving prison sentences in Northern Ireland who were the subject of false evidence or agent provocateur.
"The brass monkey attitude from two secretary of states is that it is better to see no evil, hear no evil, speak no evil - just turn a blind eye."
The Home Office said the public interest did not require Northern Ireland's inclusion in Pitchford, legal documents disclosed.
Tony McGleenan QC, for the British government, said it was open to the devolved authorities in Belfast to create a bespoke inquiry separate from that operated by Pitchford.
Mr Emmerson said national security could not be scrutinised from Belfast.
Mr Justice Paul Maguire allowed the judicial review because the issues required further investigation.
He said: "The way in which matters seem to have come forward is peculiar.
"I accept that it is an oddity that the decision of the home secretary seems to come in the form of a reply to a pre-action protocol letter."
Anti-globalisation campaigner Jason Kirkpatrick, who says he was a victim of abuses by the Met's undercover unit, is taking the court challenge and said the decision was a step in the right direction.
He said: "The truth needs to be exposed about what these police units have done to us."