Iain McMillan, the director of CBI Scotland, last week said that a meeting of 16 of its members was ''at one'' with support for an early ballot after meeting Scottish Secretary Michael Moore in Edinburgh.
However, four of the 16 businesses at the meeting to discuss the referendum have told the Sunday Herald they had not backed an early poll.
Last night McMillan accepted there had not been unanimity and that some companies said nothing. He said the "most commonly occurring view expressed" had been for an early vote.
The SNP claimed the CBI Scotland boss had been caught taking the companies' names in vain. Among those present at the meeting were international firms such as Barclays Wealth and the Edrington Group, which owns some of Scotland's most famous whiskies.
The event led to widespread reporting about business leaders wanting an early referendum. However, four of the firms present have since told the Sunday Herald that was not their view.
One businessman said it was "absolutely not the case" that all the firms wanted an early vote, and that there had been a broad range of opinions.
McMillan was also criticised for exaggerating opposition in the business community during the 1997 referendum on devolution.
He claimed all 54 CBI council members had agreed a new Scottish Parliament with tax-raising powers would "damage business north of the border" despite only 24 attending the relevant meeting.
The latest row concerns a round table lunch organised by the CBI last Monday at Edinburgh's Roxburghe Hotel, at which Moore met firms as part of the UK Government's referendum consultation.
Afterwards, in an echo of his 1997 comments, McMillan said those present had agreed the referendum should be before 2014.
He said business would be "content" with 2013, but would prefer the vote to be "fast-tracked".
CBI Scotland also issued a press release titled "2014 is too late for Scottish independence vote, say CBI members" which quoted only McMillan.
In it, he said: "This was a broader turnout from membership, and the mood in that regard was very much at one with the position of the council of CBI Scotland – and that is that the referendum should be held sooner rather than later.
But several firms denied this.
Barclays Wealth said it was "absolutely not" their position, as the group was politically neutral.
In an official statement issued to the Sunday Herald, it said: "Barclays is agnostic on the timing of a referendum on Scottish independence and has never expressed a view on this subject."
A spokesman for Edrington, which owns The Famous Grouse and Macallan brands, said: "Edrington didn't express any views at the meeting. We were there to listen to the Secretary of State outline his thinking on the consultation."
Martin McAdam, chief executive of Edinburgh-based wave energy company Aquamarine Power, said it was "absolutely not the case" there had been agreement on timing, and he had told the meeting he felt strongly it was for the SNP Government to decide.
"I have no idea how he [McMillan] came to arrive at that. There's no way that I could say that all the members who were present at the meeting had a single view in relation to the timing of the referendum. That was not the case."
He added that while business would naturally have a view on a referendum, the process "should not be driven by business, but by political, cultural and historical reasons" as businesses had no votes. "The fate of any referendum should be with the people of Scotland," he said.
The Law Society of Scotland, which was also among the 16 CBI members at the meeting, said it had not yet formed a position on the referendum timing.
Chief executive Lorna Jack said: "The Society has not publicly expressed its view on the referendum, apart from to say that the legal position is not clear but we will be responding to the referendum consultations."
SNP MSP John Wilson, deputy convener of Holyrood's Economy Committee, said: "It's clear CBI Scotland's comment misrepresented some of the businesses it represents.
"It is important the debate on Scotland's future is done in an open and honest way, and that those who represent organisations don't let their personal opinions interfere with their professional role. Companies should not be misrepresented in this way."
McMillan denied misrepresenting the views of CBI Scotland members, and also that his own views had coloured his statement: "I have no personal view on this. I have no personal prejudices. My business is business advocacy to represent the views of the CBI."