The changes, known as English votes for English laws or Evel, are also “over-engineered and potentially burdensome” and should be piloted before being introduced fully, the House of Commons procedure committee said.
Former prime minister Gordon Brown has previously said the change could hasten the break-up of the UK by creating two classes of MP and fuelling SNP calls for independence.
The UK government will push ahead with the plans this week when they will be brought before MPs. But the SNP said the committee’s report exposes the “utter confusion and total inadequacy” of the plans and demanded a re-think.
The SNP’s Westminster leader, Angus Robertson, said: “The Tories have got themselves into a first-class muddle and are trying to force this through, with too many flaws, too quickly.
“English Votes for English Laws puts forward an absurd solution to the UK’s current constitutional inequalities and it is clear that the proposals need to go right back to the drawing board so that they can be examined properly.”
A key change is the introduction of a new parliamentary stage for laws that do not affect other parts of the UK.
English or English and Welsh MPs would scrutinise such legislation alone and then accept or veto it before a final reading in front of the whole House, including Scottish MPs.
Speaker John Bercow and House of Commons officials would decide what constitutes English-only legislation, which procedure committee chairman Charles Walker warned could prompt legal disputes.
Mr Walker said: “Legal challenges to the decisions of the Speaker and to the procedures of the House, though unlikely to succeed, cannot be ruled out.
“It is important that legislation be drafted as clearly as possible to meet the tests for certifying England-only legislation.”
Mr Bercow should not have to give reasons, and should be able to use his discretion for certifying what qualifies as English legislation, the committee said, to protect the Speaker from being drawn into “political argument”.
The SNP said many issues that would appear to only be to do with England and Wales, such as health, could have a knock-on effect for Scotland’s budget.
Mr Walker added: “The committee has recommended changes which will give the whole House a say in how it applies these procedures, and will streamline the process required to allow colleagues from constituencies in England or England and Wales to vote on legislation which affects those constituencies only.
“Clearly the proposals represent a substantial change to the House’s procedures, and they ought to be piloted on statutory instruments, and a small number of bills, before they are fully implemented.”
Labour’s shadow Scottish secretary Ian Murray said the report showed the plans are an “incomprehensible mess”.
He said: “This report adds to the many expert voices who have already said that these proposals will not strengthen Parliament. Instead, David Cameron’s proposals will weaken our democracy, weaken Scotland’s voice in Parliament and for the first time create two classes of MPs. It could lead to the perverse situation where some unelected members of the House of Lords will be more powerful than elected MPs.
“Labour will put forward our own proposals that will simplify this process, but not threaten the way the UK’s democracy works.”
The committee report said the changes it has called for will give all MPs a say in how the procedures are applied and will “streamline” the system for voting on England-only or England and Wales only matters for MPs in those constituencies.
MPs are due to vote on a revised set of proposals on Thursday.
Scotland Office minister Ian Stewart said the government has redrafted the original plans to provide “maximum clarity and transparency”.
He said: “When the new proposals are published this week that will reflect a number of the changes that were suggested but keep the basic principle.
“The arguments for setting up the Scottish Parliament were that if a measure applied solely to Scotland, then Scottish MPs should have the final say on it. This applies the same principle for England: if the matter applies only to England … then it would have to be consented by members in England.”