Ministers face a fresh rebellion this week over plans to allow court cases affecting national security to be heard behind closed doors – despite claims that they have "substantially rewritten" the proposals to head off protests from Liberal Democrats.

The controversial Justice and Security Bill returns to the House of Commons tomorrow, two months after it was defeated in the House of Lords. A senior government source revealed yesterday that key sections of the Bill had been redrafted following the bruising encounter "to accommodate the Liberal Democrats". Kenneth Clarke, who is in charge of the Bill, had accepted key changes, notably restrictions on the use of the "closed material procedures" (CMPs), which would allow cases to be heard in secret.

But the Conservative backbencher Andrew Tyrie dismissed the claims, and called for more fundamental concessions before the Bill is allowed to pass into law. Mr Tyrie, who will publish a pamphlet tomorrow warning that the "secret justice" proposals would prevent disclosure of practices including torture, said: "The title of the Bill is classic doublespeak; it brings us neither more justice nor greater security. To agree only to the amendments suggested by the Lords is not going far enough, as the Lords simply did not have the time to put all their concerns over this Bill in the form of amendments."

Download the new Independent Premium app Sharing the full story, not just the headlines

Ministers presented their proposals to allow national security evidence in some civil cases to be heard in secret for the first time in an attempt to protect the Government from having to settle out of court rather than risk sensitive information becoming public. Mr Clarke claimed the laws are necessary because terrorists are launching a "steady stream" of multimillion-pound compensation claims against the security services.

Supporters also claimed the current system – under which the Government must apply for a public interest immunity (PII) certificate to allow sensitive material to be excluded –needed to be reformed. But the Bill threatened to open a split within the coalition, particularly after the proposals were defeated – against the wishes of the party leader Nick Clegg – at the Lib Dem conference last year.

Critics pointed out that the "secret justice" measures could have been used to suppress revelations about the ill-treatment of UK residents and terror suspects Binyam Mohamed and Bisher al-Rawi, and Afghan farmer Serdar Mohammed. Donald Campbell of the human rights group Reprieve said the Bill could also prevent disclosure of key details in military compensation cases.

In November, the House of Lords forced through amendments that removed a secretary of state's exclusive right to apply for a secret hearing and gave judges more discretion to decide whether hearings should be held behind closed doors.

A government insider said Mr Clarke had bowed to concerns raised by the Lords and by Parliament's Joint Human Rights Committee (JCHR). The source said: "The Bill is being substantially rewritten to accommodate the Lib Dems and clauses have been rewritten to achieve what the JCHR wanted. The Bill will accept that judges may, rather than must, consider a CMP."

But it was clear that the concessions would not be enough to assuage the Bill's critics. Mr Tyrie and a vocal band of colleagues are calling for further measures, including allowing judges to exhaust the PII system before considering a CMP, imposing a "sunset clause" limiting the time the powers would be available to ministers, and enabling a judge to balance the "interests of justice" against national security in deciding whether information can be disclosed.

Lib Dem MP Mike Crockart, who sits on the committee that debates the Bill this week, has also proposed amendments including a requirement for the new system to be monitored by the independent reviewer of terrorism legislation.

He said: "The question was really whether the proposed response was proportionate and I was clear that the balance wasn't right. The Government must not try to roll back the changes made in the Lords."