The government has won a vote to keep the House of Commons debate on whether to ratify the Lisbon Treaty to 12 days.
Opposition parties wanted the debate to last 18 days
Opposition MPs had called for 18 days, but the motion passed by 299 to 243 - a majority of 56.
During a six-hour debate on the EU (Amendment) Bill's timetable, the Tories accused the government of having a "cynical approach" to making policy.
But Europe Minister Jim Murphy gave a "guarantee that Parliament can scrutinise the Lisbon Treaty".
Earlier, a Conservative amendment to allot 18 days to debate the bill - to ratify the treaty - failed by 59 votes.
The Tories and some Labour MPs say there should be a referendum on whether the UK adopts the treaty, while the Lib Dems want one on whether the country stays in the EU.
The government says Parliament should decide whether to ratify the treaty, as it does not have significant constitutional implications.
MPs begin debating the content of the treaty on Tuesday, with the early focus on home affairs and justice aspects.
On Monday, the government was criticised by opposition and some Labour MPs over its timetable for the bill.
Shadow foreign secretary William Hague said the government had pledged plenty of time for line-by-line scrutiny but just 45 seconds was available for each line.
He added: "Ministers, it seems, are engaged not only in trying to hide from Parliament the extent of what they have agreed to, but they are also engaged in hiding from Parliament the extent of what they have not yet agreed to but intend to sign up to once these debates are out of the way."
Mr Hague also said: "There could not be a more cynical approach to the conduct of government policy, deeply lacking in openness, transparency or honesty."
Lib Dem spokesman Simon Hughes insisted the timetable was even alienating supporters of the legislation.
He added: "The modernising tendencies of the government wanting to do something good in terms of procedure have been overridden by the old tendency ... of the Stalin in Number 10 and his friends wanting to be very authoritarian about the timetable of this bill."
Senior Labour MP Gwyneth Dunwoody said the treaty's transfer of powers from the Commons to European institutions on transport issues was not even mentioned in the government's daily subject headings for debate.
And Labour former minister Frank Field said some on his side felt a "certain apprehension" at the government's approach.
But Mr Murphy said the issues could be raised during debates on the single market and EU institutions.
He told MPs: "We aim to guarantee that Parliament can scrutinise the Lisbon treaty."
Mr Murphy added: "The government tabled this motion to ensure that those inside and outside the House have a clear timetable which sets out when important issues relating to the treaty will be considered."
He added that 12 days was equivalent to the combined time given to the treaties establishing the Single European Act, the Amsterdam Treaty and the Treaty of Nice.
Under the government's timetable there will be separate debates on issues like cross-border crime and justice; energy; human rights; climate change and the single market.
The opposition wants more time for further debates on issues like the Charter of Fundamental Rights and provisions concerning national Parliaments.
MPs are due to be given different amounts of time each day to debate the bill - ranging from one and a half hours to discuss the measures on day two, to six hours during the bill's remaining stages in the Commons on day 12.
Prime Minister Gordon Brown signed the treaty in December but Parliament must ratify it.
It replaces the EU Constitution, which was abandoned in 2005, but on which Labour had promised a referendum.
Opponents led by the Conservatives accuse Labour of breaking their promise by not holding a referendum on what they say is essentially the constitution under a new name.
The government argues that the two documents are very different and that Parliament should scrutinise the treaty.
Prime Minister Brown is due to host an economic summit in Downing Street on Tuesday with the leaders of France, Germany and Italy.