A source said Labour chairman Hilary Benn had tried to "bounce" members into agreeing a 155-page report into the government's Brexit White Paper.
BBC political editor Laura Kuenssberg said the source had told her the report could not be allowed to stand.
The committee's press spokesman declined to comment on the claims.
According to the source, there had been no consultation on the committee's report - drawn up after a number of evidence sessions held in Parliament - before Mr Benn put it forward to a vote.
The report, which has yet to be published, was into the White Paper which sets out the themes of the government's goals for its negotiations with the EU.
These include:
The Exiting the European Union Committee was appointed by the House of Commons to scrutinise the expenditure, administration and policy of the Department for Exiting the European Union.
It has a 21-strong membership, made up of MPs from all parties, including Labour, the Conservatives - including ex-cabinet ministers Michael Gove and John Whittingdale - the Scottish National Party, Liberal Democrats, Plaid Cymru and the Democratic Unionist Party.
Mr Benn - a Remain supporter during the referendum - was elected to lead the new select committee last October, beating Leave campaigner and fellow Labour MP Kate Hoey to the job.
The role of select committees, which interview witnesses and produce reports to check the work of different areas of government, has increased in profile in recent years.
Committees are often split along party lines and in some cases have been known to publish "minority reports" where a faction disagree with the majority view on an issue.
It is not known yet whether those who disagree with the proposed report will produce their own one.
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A number of Brexit-backing MPs walked out of a private meeting of the Commons Brexit Select Committee in protest at a report they claimed was "too gloomy".