The Prime Minister is facing a showdown with peers this autumn over plans to extend detention without charge to 42 days after a Lords committee described them as muddled and said that they could lead to the collapse of terrorism trials.

In a report today the House of Lords Constitution Committee says that the proposals - under which Parliament would vote on allowing an extension to the pre-charge time limit beyond 28 days - blur the lines between the judiciary and the legislature. The plan “arguably risks undermining the rights of fair trial for the individuals concerned”.

The Counter-Terrorism Bill is expected to return to a House of Lords committee in early October, followed by a full vote later that month.

In June MPs passed the measure by nine votes, in the face of a Labour backbench revolt and Conservative and Liberal Democrat opposition. At the Bill's second reading in the Lords the vast majority of speakers opposed the proposal, Baroness Manningham-Buller, the former Director-General of MI5, making a pointed intervention.

Today's report gives further arguments to the Bill's opponents in the Upper House. The Labour rebellion may include Lord Falconer of Thoroton, the former Lord Chancellor, and Lord Goldsmith, the former Attorney-General.

Under the legislation, MPs and peers would vote on whether to grant a temporary “reserve power” for the Home Secretary, allowing courts to authorise detention for up to 42 days were there an operational need. Although the reserve power order would not be specifically about an individual case, politicians would “have to tread a tightrope” to avoid prejudicing any trial, the peers say in today's report.

“We are unconvinced that the Government have properly thought through this aspect of their proposed scheme.”

The committee was also concerned that a judge could have to decide whether to extend a suspect's detention within hours of a “highly politically charged debate” in Parliament.

“There is a risk that this will be perceived to undermine the independence of the judiciary.”

The Government's desire to increase democratic accountability was understandable, but risked “conflating the roles of Parliament and the judiciary, which would be quite inappropriate”.

The peers added: “Far from being a system of checks and balances, this is a recipe for confusion that places on Parliament tasks that it cannot effectively fulfil and arguably risks undermining the rights of fair trial for the individuals concerned.”

Plans for the Home Secretary to brief the chairmen of three key parliamentary committees confidentially about the need for reserve power orders were “untenable” and should be scrapped.

The peers also said the “elaborate” decision-making process would give a far greater opportunity for legal challenges. “It is a weakness of the Bill, not a strength, that it is likely to lead to high-profile litigation during a time when the response to terrorism will be a matter of high controversy,” the report said.

The peers also expressed concerns about the Home Secretary being given power to direct that sensitive inquests should be heard without a jury.

In a letter to the committee, Admiral Lord West of Spithead, the Security Minister, signalled a government concession, stating that a “sunset clause” whereby the measure would need to be renewed after a certain time was being considered.

Lord Goodlad, the committee's Conservative chairman, said: “We are concerned that some of the proposals being put forward by the Government in the Counter-Terrorism Bill would place inappropriate responsibilities on Parliament.” Politicians would be asked to act in a “quasi-judicial manner” in deciding the pros and cons of extending the limit beyond 28 days.

“Considering that any debate will be highly political in nature and any vote may well be whipped by the political parties, we are deeply concerned that the independence of the judiciary may appear to be undermined and that trials may be prejudiced,” Lord Goodlad said.

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