The DUP was "shocked" by what it learned in a meeting with decommissioning chief John de Chastelain, Ian Paisley has said.
Ian Paisley said his party now wanted to meet the government
He said the two church witnesses to disarmament were "IRA nominated" and the party now wants to meet them.
Senior Ulster Unionist Danny Kennedy said Mr Paisley was "wrong to question the honesty and integrity of the church witnesses to IRA decommissioning".
Sinn Fein's Gerry Adams said Mr Paisley would need time to digest the move.
"His concern is (about) a process of change and... because he has lived and built a career on frightening people and on crisis," he said.
"(It is) a concern that the future isn't going to be good for unionism.
"The future is going to be good for everyone on this island, so we have to give Ian Paisley a wee bit of space."
After meeting General de Chastelain on Tuesday, Mr Paisley said Catholic priest Father Alec Reid and ex-Methodist president Rev Harold Good were not appointed by the government or arms body.
The party said the list of IRA weapons had been "revised and tampered with".
"These are the things that put a very big question over what has taken place," said Mr Paisley.
The DUP is now seeking a meeting with the British government.
It has questioned if the inventory list given by the intelligence services was accurate or "just cobbled together" for political expediency.
Mr Paisley claimed there had been a cover-up.
"We discovered that the witnesses turned up in the presence of the IRA. None of the commission heard from the government who the witnesses were," he said.
"Nor did the government certify them - they were not appointed by the government.
"It was suggested that the commission appointed them. The commission said no... they came and introduced themselves in the presence of the IRA and they said 'we are the appointed witnesses'."
Mr Paisley said he was told some of the IRA's weapons had already gone to dissident republican groups.
UUP assembly member Danny Kennedy said it was "sad" that Mr Paisley had "cast aspersions on the character and integrity of the two witnesses to IRA decommissioning".
He added: "It is essential that an inventory of the IRA's decommissioned weaponry is published and that the republican movement's vast criminal empire is dismantled."
Speaking after his party's meeting with the arms body, SDLP chairman Alex Attwood said they felt "more reassured" that what was said in relation to IRA weapons had happened.
"Anybody who thinks they can make a fool of what those three men are trying to do and what the witnesses saw happen is very badly misled and misguided," he said.
Mr Attwood said that the issue of loyalist weapons was also raised and the party had encouraged the commission to keep working to bring about a situation where loyalist paramilitaries might act.
General John de Chastelain is meeting a number of politicians
Prime Minister Tony Blair said the completion of IRA decommissioning was the result of "a lot of hard work", which was worthwhile if it brought lasting peace.
In his keynote speech to the Labour Party conference in Brighton, he said: "There's a lesson for Northern Ireland - nothing good comes easy."
Earlier on Tuesday, Northern Ireland Secretary Peter Hain said unionist distrust was "natural", but the IRA's "historic move" brought the return of devolution closer.
Sinn Fein's Martin McGuinness is going to the US to brief Irish Americans.
'Sceptical and suspicious'
Mr Hain said he could understand Mr Paisley's scepticism, but asked him to respect the integrity of General de Chastelain.
Gerry Adams said people need time to absorb the news
"I wouldn't have expected Ian or the unionists to just bowl over and welcome everything with open arms because they've got a lot of cause to be sceptical and suspicious over the behaviour of the IRA in the past," he told BBC News on Tuesday.
"The IRA have often promised to do things and then reneged on them."
The Independent Monitoring Commission (IMC) reports next month and in January would consider whether the IRA was delivering on its promise to cease paramilitary and criminal activity, Mr Hain said earlier.
The White House has welcomed the IRA's move as an "important first step" and the US State Department called on all paramilitary groups, whether loyalist or republican, to work with General de Chastelain to bring about complete disarmament.
Making his report on Monday, General De Chastelain said he had handled every gun and made an inventory of the ordnance, which was in line with estimates provided by the UK and Irish security services.