MPs voted by 298 to 261 in favour of extending legislation to permit fracking 1,200 metres (4,000 feet) below national parks, areas of outstanding natural beauty and world heritage sites with drilling taking place from outside the protected areas.
Environmental campaigners and opposition lawmakers accused the government of using "sneak" tactics to relax the legislation.
The issue was discussed and approved in committee only on Tuesday and the vote was held under a procedure normally used to speed minor parliamentary business.
Opposition MPs criticised the rush to back fracking, a way of extracting gas by pumping water, chemicals and sand underground that opponents say could pollute water supplies, scar the countryside, and trigger earthquakes.
Liberal Democrat leader Tim Farron said the government was trying to "sneak" through a decision, labelling such a move "outrageous".
The change would allow shale gas companies to drill sideways under national parks. Before the general election, the government had made a commitment for an "outright ban" on drilling in national parks.
"It's not even a year since the government promised to ban fracking in national parks," Hannah Martin, energy campaigner at Greenpeace, said in a statement.
Friends of the Earth said the government was "pushing through" the changes without a full debate, adding that the rules could endanger drinking water aquifers.
"People won't be fooled by the government's blatant attempt to get around their promises on a technicality -- fracking under a national park does not equate to an 'outright ban'," said Rose Dickinson, energy campaigner for Friends of the Earth.
Prime Minister David Cameron's government has pledged to go "all-out for shale", saying it would increase energy security, keep prices down and create jobs.
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