It was among documents recently declassified in Dublin under the 20 and 30-year rules.
However, the file has now been withdrawn, according to The Irish Times, who reported it was at the request of Ireland’s Department of Foreign Affairs.
The department, Sinn Fein and Mr Kelly have all been contacted for comment.
According to The Irish Times, the file was pulled following “urgent consultations between the Department of Foreign Affairs and the Department of Justice” in the Republic.
Government files are released annually under the 20 and 30-year rules in Dublin, as well as in London and Belfast.
They contain previously confidential summaries – often frank in nature – of political and security issues from the time.
The Irish Times reported that files in Dublin are carefully vetted by senior and retired officials before release, and can be withheld if deemed to be against the public interest.
However, there has been no explanation as yet about why the file with the references to Mr Kelly has been withdrawn.
It contained a letter, written by assistant garda commissioner Noel Conroy, which identified Mr Kelly as “the most dominant figure” within the Provos in the 1990s.
The North Belfast MLA has taken a number of libel actions over reports about IRA activities.
He previously rubbished a classified British document, which formed part of the UK’s State Papers, which claimed he had been put in charge of the IRA reorganisation to ensure centralised control for the peace process. Mr Kelly said the allegation was “not true”.
Mr Kelly had served a prison sentence for the 1973 Old Bailey bombing before escaping from prison. He became a Sinn Fein politician and played a central role in the peace process and 1998 Good Friday Agreement.
Mr Kelly is one of two MLAs – the DUP’s Edwin Poots is the other – to still be a member of the Assembly.
Mr Conroy, who would go on to become garda commissioner in 2003, wrote the briefing note to the Irish Department of Justice on May 21, 1996.
The letter was addressed to the department’s secretary general Tim Dalton and formed a two-page security analysis of the leadership of the IRA.
It said: “The current PIRA [Provisional Irish Republican Army] strategy continues to be dominated and controlled by the leadership of Gerry Kelly, Belfast; Brian Keenan, Belfast; Martin McGuinness, Derry; Pat Doherty, Donegal; and Thomas ‘Slab’ Murphy, Louth. Gerry Kelly is emerging as the most dominant figure within this group.
“Martin Ferris is also emerging as highly influential in formulating strategy and is consulted and advised by the northern leadership on all major issues.”
In 1996 Mr Conroy was serving as the head of the garda’s critical Crime and Security branch.
The letter notes that there was “growing dissatisfaction amongst many” members of Sinn Fein and the IRA about “the non-consultative attitude of the current leadership of both organisations”.
There is a growing feeling at grassroots level that the leadership is out of touch
“This is particularly evident in the Cork/Kerry, Limerick and Dublin regions. The constitutionality of the decision within Sinn Fein on the Mitchell Principles is being questioned.
“However, the Adams leadership has the approval of the Ard Comhairle of [Sinn Fein]. There is a growing feeling at grassroots level that the leadership is out of touch.
“Indeed, there are cynical comments about their ‘infallibility’ being expressed. This feeling is more marked in the south with Northern Units being more supportive.”