The Government's attempt to replace self-regulation of MPs' financial affairs by a new independent regulator faces an unexpected challenge. Ministers hope to push the Parliamentary Standards Bill through the Commons in three days this week. But they face the challenge of an outspoken memorandum by Malcolm Jack, Clerk of the Commons. This questions ministerial claims about the Bill's impact on parliamentary privilege: MPs' long-disputed right to free speech without the threat of judicial action as enshrined in the Bill of Rights of 1689.

On Thursday, Harriet Harman, the Leader of the Commons, told MPs that "the question of parliamentary privilege is not an issue in the Bill". Not so, says Mr Jack: "Since the Bill seeks to make statutory provision in relation to matters whcih fall within Parliament's exclusive cognisance or may affect proceedings in Parliament, it affects the established privileges of the Commons, thereby upsetting the essential comity established between Parliament and the courts."

The memorandum, viewable on the website of the Commons Justice Committee, is already causing a stir at Westminster. It may force the Government to make concessions, not least since some peers are getting agitated and starting to harumph about a threat to the constitution. The Lords is not included in the Bill but peers are protesting now because they fear a similar model will be applied to them before long.

The Government argues, with broad support from the two main Opposition parties, that the public no longer trusts MPs to regulate themselves, hence the need for the new Independent Parliamentary Standards Authority with sweeping powers and a separate investigator. Ministers argue that judicial challenges should be very rare given the approval by MPs of the Code of Conduct and an appeals mechanism.

Mr Jack is less optimistic. References in the Bill to a code of conduct would make it justificable and "in the present climate there might be no shortage of potential litigants trying to make a point". He argues that it is unclear why this clause is in the bill. "If its effect would be minimal, then it cannot really be needed. If it would have a significant effect, then the risk of litigation affecting the boundaries of jurisdcition between the courts and Parliament is substantial."

Further clauses, he argued, could limit the House's use of disciplinary sanctions, while provisions about parliamentary proceedings would "have a chilling effect on the freedom of speech of members and of witnesses before committees".

Mr Jack offers an alternative to piecemeal tinkering via a new law updating parliamentary privilege along the lines recommended by a Joint Committee of both houses in 1999. This would define Parliament's control of its own affairs, along the lines already adopted in Australia.

But, not for the first time, speed is the enemy of adequate scrutiny, risking the type of consequences raised by Mr Jack. Gordon Brown is determined that this Bill to "clean up politics root and branch" should become law before Parliament starts its long summer recess in three weeks. It would be far better for Parliament to return for a couple of weeks in September to allow time for proper debate.

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