Gordon Brown has rejected calls to block a controversial move by MPs to get out of freedom of information laws.
Mr Brown has pledged to respect MPs' decisions
MPs pushed the plan closer to becoming law earlier in what critics called a "shameful day for Parliament".
The MPs say they want to protect private letters from constituents - but critics say the move would also allow them to keep their expenses secret.
Mr Brown, who takes over as Labour leader and prime minister next month, has pledged more "open" politics.
A spokesman for the chancellor said he had also promised not to dictate to MPs.
"Gordon has also spoken about the sovereignty of Parliament. If MPs have voted this measure through then that is a matter for them", his spokesman said.
Critics say despite its neutral stance, the government is in favour of the Private Members' Bill and has allowed it the time to progress through Parliament.
Liberal Democrat MP Norman Baker, who has led calls to block the Freedom of Information (Exemption) Bill, claims MPs were prevented from debating it more fully earlier, saying the events made him "ashamed to be an MP".
He is to make a formal complaint to the Commons speaker after MPs voted for the bill, by 96 to 25, to give the bill a third reading. It will now proceed to the Lords for further consideration.
Mr Baker and fellow critics had hoped to "talk out" the bill by using up all its allocated time in the Commons, but after a five-hour debate, and with five minutes to go before time ran out, supporters voted for it to proceed to the Lords.
If passed, the FOI bill would effectively remove both the Commons and House of Lords from the list of public authorities obliged to release information under the 2000 act, which came into force in 2005.
The bill also protects all MPs' correspondence from release and stops authorities, such as councils or companies, confirming or denying whether they have received a letter from an MP.
During the debate, Mr Baker described the Freedom of Information Act as "a flickering candle" which "could be extinguished in many ways" by the bill.
"Let me make it plain the best solution entirely is that this bill doesn't go through because the present arrangements are working really quite well and there is no need to change them."
After the vote, he vowed to continue his fight to block the bill.
"It is an effrontery for the House of Commons to make the deeply hypocritical move of exempting itself from a law that applies to every other public body in the country."
He continued: "It is also deeply undemocratic that MPs on both the government and Conservative benches have clearly collaborated to ensure that those with a contrary view, fighting for open government, were silenced after barely any debate on amendments to the bill."
Several ministers voted in favour of third reading, including Caroline Flint, Phil Woolas, Joan Ryan, Meg Munn, Ian McCartney, Tony McNulty, Parmjit Dhanda, and Maria Eagle.
Members of the backbench committee of the Parliamentary Labour Party have also emailed colleagues to say they "feel strongly" that the bill's measures were "worthy of support".
Tory backbencher David Maclean, who is sponsoring it, said it would protect MPs' correspondence.
During the debate, Mr Maclean said his bill was necessary "to give an absolute guarantee that the correspondence of members of parliament, on behalf of our constituents and others, to a public authority remains confidential".