Peers have begun debating controversial anti-terror legislation including plans to hold suspects under house arrest.
Mr Clarke's plans face a rough ride in the Lords
MPs have already backed the Prevention of Terrorism Bill - but only after Charles Clarke agreed greater judicial oversight of the "control orders".
The new legislation could be derailed by peers who are expected to vote on it next week.
Lord Strathclyde, Tory leader in the Lords, said ministers should expect the Bill to be "substantially re-written".
Intercept evidence call
The bill proposes "control orders", which as well as house arrest could mean curfews, tagging or bans on telephone and internet use.
They would replace current powers to detain foreign terror suspects without trial, which the law lords have ruled against.
On Monday, MPs voted 272-219 in favour of the bill after key concessions from Mr Clarke.
The government earlier saw its 161-strong majority cut to just 14 as a cross-party amendment was narrowly rejected by the Commons despite the support of 62 Labour rebels.
Mr Clarke won over critics by announcing he would introduce an amendment in the Lords to ensure the most controversial control order, amounting to house arrest, would be imposed by judges and not politicians.
The Bishop of Worcester, the Rt Rev Peter Selby, warned that the plans amounted to a "victory for terrorism".
"I see this bill as posing very serious dangers of a spiritual kind to the society in which we live," he said.
Lord Strathclyde said ministers should "prepare themselves for substantial rewriting of various aspects of the bill".
"They should consider far more seriously the use of intercept evidence in any trial and I think they should drop the most objectionable proposals, which are for house arrest."
'No desire' for concessions
But Mr Clarke told BBC Radio 4's Today programme he believed the changes he had made to the bill to win over critics in the Commons should be sufficient to satisfy colleagues in the Lords.
"No bill goes through Parliament without detailed consideration being made, but I believe that what I announced yesterday will be sufficient to secure the agreement of the House of Lords," he said.
Charles Clarke faced a Labour backbench rebellion
"I have no desire to make further so-called concessions on the bill."
Mr Clarke's proposed amendment will be debated by the Lords on Wednesday and Thursday without having been considered by MPs. The debate is unlikely to result in a vote.
The prime minister's official spokesman insisted the measures will become law.
He also defended Tony Blair's assessment that the house arrest plans were necessary because there were "several hundred" people in the UK plotting terror attacks.
"There is a difference between different levels of threat posed by people," he said.
"The government will do everything to deliver on national security."
Speaking after the Commons debate, shadow home secretary David Davies said the bill had been "clearly very badly drawn-up" and that the government was trying to rush it through too quickly.
He said it would be possible to "rescue" the government and make the law "tolerable" by amending it in the Lords.
"The scope for miscarriages of justice is enormous," he told BBC News.
Mark Oaten, for the Liberal Democrats, said Monday night's vote showed the government had "lost the confidence of all sides of the House".
He said: "They need to rethink the bill, and extend the power of a judge to decide on all control orders, build safeguards on evidence and create charges against suspects.
"Unless there is a major movement, this bill is doomed to fail."
BBC News political editor Andrew Marr said: "I think that this is a bill in deep trouble. It's been unravelling in the House of Commons - it may unravel further."
The government wants the new bill to pass into law by 14 March, when the current powers expire.