A statement from the parliament on Wednesday confirmed the changes, but said they would not affect the completion date of July next year. Sources on the design team disagreed. They said the building would not be complete until the end of August.
One source on the team, which comprises architects EMBT and RMJM, said these were "alterations and issues" connected with the building services within the parliamentary complex, especially in the debating chamber. The source said: "There are still a lot of changes being made."
However, he added that the latest changes could be paid from the £400m budget. He said an £11.8m "contingency" fund ought to cover the variations. "The budget will not change as things stand. We have our fingers crossed. We are hoping that the budget will not exceed the contingency."
Building warned in August that the programme and costing might have to be revised because of design changes in July this year.
The disclosure of the latest changes came as the appointment of construction manager Bovis Lend Lease in 1998 was being scrutinised.
Giving evidence to the Fraser inquiry on Wednesday, former Holyrood project manager Bill Armstrong said that the selection panel broke Scottish Office rules by not choosing the lowest bid on the table. Documents shown at the inquiry revealed that the Bovis tender was £926,000 more than that of rival firm Sir Robert McAlpine.
He said: "Under procurement laws, once you get the four tenders and they can all do the job, you are duty bound to take the lowest."
Armstrong added that he had had informal discussions with the chief architect at the Scottish Office, John Gibbons, over the possibility of sacking the late architect Enric Miralles less than six months after he won the contract in July 1998.
We have our fingers crossed. We are hoping the budget will not exceed the contingency
Source on design team
Armstrong, who quit in December 1998, said Miralles ignored his instructions, failed to come up with completed plans and had went over the heads of civil servants to Scottish secretary Donald Dewar.
Armstrong said he felt that once the plans for the scheme had been finalised, Miralles' architectural practice EMBT could be removed from the equation, leaving RMJM to take over full design responsibility.
He said the Holyrood scheme had already been running four weeks late just two months after Miralles won the competition to design it.
Armstrong also said senior civil servants failed to reveal significant increases in costs in 1998. He said the budget had been set at £50m in October 1998 but by November it had already reached £74m.