The changes are aimed at speeding up planning approval for big projects
Plans to streamline planning decisions on big projects like airports have been attacked on all sides of the Commons.
Paul Truswell warned of a "tremendous amount of concern" among Labour MPs over plans to hand decisions on major projects to an independent commission.
Tory MP John Redwood said it would be an "unelected quango" and said the time given to debate it was a "travesty".
Local government minister John Healey said two full days had been allocated to discuss the planning bill.
MPs are debating the Planning Bill, which largely applies only to planning laws in England. It includes a measure to take away ministers' and councils' planning powers over major projects like new airports and power stations.
Instead an Infrastructure Planning Commission (IPC) would take decisions on major infrastructure - the government hopes it will speed up approvals for big projects.
More than 60 Labour MPs signed a motion opposing the IPC and on Monday Mr Truswell said there was a "tremendous amount of concern" among backbench Labour MPs about "key aspects of this particular Bill" including the planning commission.
This is setting up an unelected quango to make extremely important decisions
He also said he was concerned that debate on sensitive issues like the planning commission were being "compressed into a two hour period next Monday night".
The amount of time set aside for debate also prompted anger among Conservative MPs.
Patrick McCormack called it "an emasculation" of the Commons and Jacqui Lait said Labour MPs' concern had forced the government to move the debate to a "graveyard slot".
Mr Redwood added: "This is setting up an unelected quango to make extremely important decisions where I, and many of my constituents, believe there should be a stronger democratic input."
He added: "It's a travesty of democracy that we should be expected to have allocated time on a range of very sensitive and constitutional matters".
The government was accused of bringing forward a bill that was "barely recognisable" from that discussed at the earlier committee stage - because of the large amount of amendments made.
Plaid Cymru's Elfyn Llywd said it was "absolutely atrocious" that 110 amendments were being "pushed through".
Minister John Healey agreed it was a wide ranging and important bill - but said that was why the government had allocated two full days for the report stage.
He told MPs he had reflected on a number of issues raised by the committee and then brought forward amendments - many of which he described as "technical".
"I have taken a judgement in allocating the time, in making sure as much time as possible for those areas likely to be of the most interest."
More than 60 Labour MPs signed a motion opposing plans for an independent commission to decide on big projects like airports and power stations.
The proposed Infrastructure Planning Commission is included in the Planning Bill, introduced last November.
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