Mr Brown, who was the chairman of Bellaghy Wolfe Tones GAA club, was locking the gates to the Co Derry club’s training ground when he was ambushed by loyalist paramilitaries from the LVF in May 1997.
He was abducted, beaten and shot six times in the head. His body was found next to a burning car.
No-one has ever been convicted of his murder.
At least four of those involved were security force informers/agents including who was under the control and direction of MI5.
Both the Brown family and SDLP Mid Ulster MLA Patsy McGlone have slammed the decision by the Secretary of State to appeal Mr Justice Michael Humphreys’ ruling that a public inquiry should be held.
The judge issued his ruling following years of campaigning by Mr Brown’s family, saying there is “a clear and unambiguous obligation” on the State to carry out an investigation into Mr Brown’s death.
The Northern Ireland Office confirmed that an appeal of the ruling was lodged earlier this week.
In a statement, a family spokesman said: “This appeal was lodged on December 31, New Year’s Eve, and there must be a suspicion that the timing was intended to bury bad news.
“Regrettably it would appear that the Secretary of State has decided that our mother will now enter her 88th year still denied the truth of how, why and by whom her husband was abducted, beaten and murdered. This is shameful.
“When the coroner abandoned the inquest early last year he recommended a public inquiry as the only legal alternative.
“The PSNI Chief Constable stated that he would not oppose such an inquiry. So it would seem that the real blockage is in London.
“The SoS has consulted with the Ministry of Defence and the Security Service MI5 before deciding to deny our family our Article 2 ECHR right to an inquiry.
“This raises profound and deeply concerning questions about collusion and the role of state agencies in this case.
“Why does the Ministry of Defence and the Security Service in London hold documentation about the murder of a totally innocent family man who was simply locking the gates of his beloved GAA club in rural Co Derry?
“What was the relationship between these bodies and the LVF leadership? What was known in advance of the murder? Why are these bodies, who have actively thwarted investigations to date, being consulted on the merits of a public inquiry?
“It is a total mystery to us why ‘national security’ has been invoked to justify the redaction of vital evidence.
“As a family we wish to put the Secretary of State on notice that we will not give up in our struggle to get to the truth. We had hoped that he would take a different path to previous Tory ministers. Sadly this would appear not to be the case.”
An NIO spokesperson said: “We have enormous sympathy for Mrs Brown and her family who have suffered so much since Sean Brown’s murder.
“The recent judgment by the High Court however raises a number of important issues, including matters of constitutional significance that go beyond this individual case.
“The Government has therefore lodged a notice of appeal to the Court of Appeal and we are seeking expedition.”
Mid Ulster MLA Mr McGlone said: “This decision from the Secretary of State flies in the face of what was a very clear ruling from Justice Humphreys that a public inquiry should be held into the murder of Sean Brown.
“Instead of acting in good faith and granting the family the inquiry they have fought so long and hard for, they issued this decision on New Year’s Eve, adding further insult to injury for the Brown family.
“All this family want is to find out what happened to their loved one and that should not be too much to ask.
“The family now face the intolerable position of months more of legal wrangling, more delay and heartache after what has been a long and emotional journey for them. I hope they can take heart from the huge support they have in the local community and right across this island. We are all behind them.
“It’s shameful that the family of Sean Brown face entering the new year still fighting for truth and justice for their beloved husband and father.”
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