The hardline unionist hit out after actor Maddy Hill, who plays Nancy Carter in the BBC soap, wore the shirt during a scene in Friday night's episode.
Mr Frazer (53) was scathing at the use of the "GAA top" – which is actually the sports kit of St Patrick's College, Ballymena.
Victims' campaigner Mr Frazer accused the GAA of glorifying terrorism, and compared the use of the shirt by the soap's producers to promoting the National Front, Ku Klux Klan or Nazism.
He posted on his Facebook account: "I'm sure many of you watched EastEnders in horror last night when Nancy Carter, who works behind the bar in the Queen Victoria, was clad in the shirt of an organisation which glorified IRA terrorists, the GAA. This surely must have been a mistake by the costume people, any shirt supporting the NF, KKK or indeed Nazism would never be allowed on a family show so why a shirt belonging to an organisation who name clubs after IRA terrorists, give out medals with IRA terrorists on them and who hold IRA events (on) their premises."
Mr Frazer, from Markethill in Co Armagh, said he had lodged an official complaint with the BBC regarding the shirt.
When it was pointed out to Mr Frazer that the top is actually that of St Patrick's College, he remained defiant.
Instead, he blamed GAA supporters for 'hijacking' the use of the shirt on the show.
"Republicans were praising it from the rooftops," he told the Belfast Telegraph.
"In fact they were saying the next thing would be the playing of republican songs in the Queen Vic. I don't see why I would have to apologise to the school.
"It wasn't the school with which the issue was raised, it was the GAA and all that goes with that."
Sinn Fein North Antrim MLA Daithi McKay criticised Mr Frazer's remarks, and called on him to withdraw them.
"The appearance of the St Patrick's shirt has created quite a buzz throughout Ballymena," he said.
"The top in question is a PE shirt."
He also added: "It is concerning that Willie Frazer continues to target anybody and everybody with an association to the GAA.
"The GAA in Ballymena, like other sports, works on a cross-community basis and Willie Frazer's comments are very much out of tune with the community in Ballymena."
A spokeswoman for EastEnders was yesterday unable to confirm how many, if any, complaints had been made regarding the shirt.
She said: "The top which Nancy Carter wore on Friday night's episode is a school PE kit which was purchased from a vintage shop.
"The character of Nancy Carter is a tomboy and wears a huge range of sportswear which she chooses for the way it looks not because she has any allegiance to any sport or club."
In 2012, the principal of a primary school described by Mr Frazer as "the junior headquarters of IRA youth" called on him to apologise to her directly.
Dera Cahalane of St Patrick's Primary in Donaghmore contacted the PSNI after Mr Frazer posted controversial remarks about her school after confusing an Italian flag flying outside it for an Irish tricolour.
The Italian flag was flying alongside Turkish and Polish flags in honour of 11 teachers from schools in Poland, Italy and Turkey who visited the Tyrone school for a European integration project.
After seeing photographs of the three flags, Mr Frazer, whose father was killed by the IRA, posted on Facebook: "The junior headquarters of SF/IRA youth, or it may as well be."
Mr Frazer told the Belfast Telegraph at the time that he apologised for a "genuine mistake".
However, he added: "If they think I'm going to get down on my hands and knees, basically the answer is no."
St Patrick's is a Catholic maintained college in Ballymena, with 500 pupils.
The college caters for both boys and girls in the 11-18 age range.
Past pupils include Hollywood star Liam Neeson and Liverpool manager Brendan Rodgers.