MPs will scrutinise the performance of London mayor Boris Johnson and his team.
Members voted in favour of setting up a regional select committee by a majority of 92.
Leader of the House Harriet Harman said the body will make the Greater London Authority (GLA) publicly accountable and guarentee value for taxpayers' money.
But some fear said the move would undermine the ability of London Assembly.
Ms Harman said: "London should not be denied the opportunity afforded to other regions to hold these bodies to account through their MPs."
However, Justine Greening, Conservative MP for Putney, said the committee would only amount to a vote of no confidence by ministers in London Assembly's ability to scrutinise the mayor.
She said: "We do need more accountability. But why spend several hundred thousand of pounds on a regional select committee for London when what people want isn't another talking shop but direct representation through being able to ask questions and get answers."
"The biggest danger we have got is it really does potentially undermine the way in which our local devolution that we have now got in London - through the mayor and the London Assembly - works and its effectiveness."
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