SNP member Pete Wishart has claimed English MPs were "driving Scotland out the door" by banning Scottish MPs from voting on English-only matters.
Constitutional history was made as some parts of the Housing Bill were voted on by English MPs alone and others by English and Welsh MPs.
"Nothing has infuriated the Scottish people more than the measures around English votes for English laws," Mr Wishart, MP for Perth and North Perthshire told the House of Commons.
Deputy Speaker Eleanor Laing warned Scottish MPs they could not vote or express a view shouting 'Aye' or 'No'.
But Mr Wishart appeared to ignore her when he was heard to shout "No".
- What are 'English votes for English laws'?
The new rules - also known as Evel - means MPs for English constituencies will be allowed to vote on matters which only affect England, instead of allowing Scottish, Welsh and Northern Irish MPs a say.
Other matters which involve both England and Wales will be voted on by MPs from England and Wales.
The Speaker of the House of Commons - currently John Bercow - will decide on whether the bill in question only affects these nations, and will be able to give his reasons for his decision.
He may also use two senior MPs to help him decide.
MPs from across the United Kingdom will still have to pass the legislation at later stages of law-making.
The proposals were first put forward by David Cameron as part of the negotiations ahead of the Scottish independence referendum, when he promised more devolution for the Scottish parliament - but also more powers for English MPs.
- What's the point?
The rules were introduced to try to tackle the so-called 'West Lothian question' - the anomaly in which Scottish MPs in Westminster were allowed to vote on matters such as health and education in England.
Because these subjects are devolved to the Scottish Parliament, English MPs did not have the same involvement in the same matters in Scotland.
Commons leader Chris Grayling argued that it was not "tenable" to have devolution to Scotland, Wales and Northern Ireland while England had no powers of its own at all.
- What are the objections?
The SNP's Pete Wishart is among those to speak out in criticism of the rules.
As a Member of Parliament, but not a Member of the Scottish Parliament (MSP), he claims it creates two classes of MP within Westminster.
He has argued that the move pushes Scottish people further towards independence.
The DUP of Northern Ireland has also critcised the rules for threatening "the fabric of our union", as has the Labour party, which also critcised them for being too complicated.