Giving evidence to a House of Commons committee, the minister said the government will have the final say on who oversees regional planning.
Under the proposals the secretary of state for transport, local government and the regions will have the power to decide if schemes 'of national significance' are considered by MPs.
The move is driven by a desire to avoid lengthy public enquiries, such as over Heathrow's fifth terminal, and the government envisages projects such as power stations, radioactive waste disposal and reservoirs being handled by Parliament.
Before the parliamentary stage there will be public consultation, with objections laid before MPs.
Questioning the minister, Labour MP Louise Ellman wanted to know if MPs would be whipped on planning decisions, even though this was banned in councils.
'Why are there going to be different rules for Parliament?' she said. 'Will there be proper scrutiny or will the whips impose the will of the government?'
Lord Falconer said many of the projects will be government policy so it was appropriate to use the whip. 'I imagine in some cases it will be whipped business,' he told the transport, local government and the regions committee.
Ms Ellman repeatedly asked the minister who will have the ultimate power over the proposed regional planning bodies.
The government plans to set up unelected bodies to oversee regional spatial strategies once county councils have been stripped of their powers.
This body will comprise a mixture of councils, regional development agencies, business and the voluntary sector.