Charles Kennedy, the former leader of the Liberal Democrats, makes an impassioned plea to Labour MPs to join a "progressive alliance" to defeat Tory rebels who want to block reform of the House of Lords.

Amid fears that the most wide-ranging Lords reforms in a century will be thrown off course , Kennedy uses a Guardian article to call on the Labour party to avoid playing "political games" by siding with the rebels.

Nick Clegg, who endured his most hostile parliamentary reception as he described the House of Lords as a "flawed institution", is concerned that his reform plans will suffer a near fatal setback.

Ed Miliband is planning to support the House of Lords reform bill at its second reading. But he is ordering Labour MPs to join forces with Tory rebels, 74 of whom signed a letter denouncing the reforms, to vote down a "programme motion" for the bill.

At least two ministerial aides are expected to resign or be sacked on Tuesday when they rebel against the government. Conor Burns, aide to the Northern Ireland secretary, Owen Paterson, and Angie Bray, aide to Francis Maude, have said they will join the rebels.

Rebel leaders, who say they have the support of 100 Tory MPs, would need only around 50 to defeat the government if they have Labour's support. Clegg fears that without the programme motion, which sets a timetable for the bill, his reforms will be talked out by Tory MPs.

A defeat for Clegg would throw the coalition into one of its gravest crises. Clegg has warned David Cameron in private that he may block his plans to reduce the House of Commons from 650 to 600 MPs if he believes that the Tories have failed to do enough to persuade their MPs to support his reforms.

Kennedy makes clear today that the Lib Dems' immediate focus is on Labour MPs as he calls on them to seize the best chance in a century to ensure that the second chamber is mainly elected. Telling Labour MPs that he shares their misgivings about the coalition, he writes: "Make no mistake, this bill is ­transformative, and we have the chance to make a giant leap.

"Whatever you think of Nick Clegg, the Lib Dems or the coalition government, the fact remains that a historic opportunity that progressives have yearned after for a century is within our grasp. This is not the time for Labour to play political games. It is now or very likely never. Tonight, a progressive alliance can defeat the Conservative rebels who are determined to defend the establishment. Together, we must take that chance."

But Sadiq Khan, the shadow justice secretary, confirmed that Labour MPs would vote against the programme motion. "The bill before us today should be allowed to be fully debated and there should be no guillotining of debate by the government," Khan said.

Labour increased the pressure on the government to relax the programme motion by pointing out that Cameron had criticised the practice of placing a time limit on bills in his maiden speech in 2001. The future prime minister said: "I cannot see how deciding in advance how much time should be given to a bill and systematic guillotining can help in that regard."

The Lib Dems pointed out that Labour imposed programme motions for the bills establishing the Scottish parliament, the Welsh assembly and the Northern Ireland assembly. One source said: "Is Labour saying devolution is less significant than Lords reform?"

Clegg, who is planning to allow MPs to debate the bill over 14 days, had indicated that the government was prepared to give MPs more time to examine the bill if Labour agrees to a programme motion. But he indicated on Monday that he has given up on these negotiations after Peter Hain, the veteran Labour campaigner who supports Lords reform, told the Guardian that he would vote against the programme motion as a way of blocking the government's wider legislative programme.

Clegg said: "Labour's ulterior motive appears to be to disrupt the rest of the government's business. That is not a legitimate way of dealing with a programme motion, which is a perfectly reasonable way for the government to try to make progress on this important piece of legislation without disrupting all other parts of our business."

He tried to reach out to Labour MPs by offering time during the committee stage of the bill to debate holding a referendum on the reform plans, and giving MPs a chance, after the first round of elections to the new house in 2015, to vote on whether to slow the process.

Aides said that Clegg was only proposing a debate on these ideas, which he would oppose in any vote.

Kennedy said that using Lords reform to give Clegg and the coalition a "bloody nose" amounted to "cynical short-termism of the most counterproductive kind". He added: "Ed Miliband is preparing to order his MPs to vote against this motion. Be under no illusion that this is anything other than a cynical wrecking move – a way of appearing to be pro-reform while making it virtually impossible for the government to proceed."