Environmental groups fear there are few safeguards left for most of Manitoba's waterways because new federal legislation would remove all but six of them from navigable waters protection.

As part of its omnibus budget bill, the federal government plans to amend the century-old Navigable Waters Protection Act to limit its reach to fewer than 200 waterways nationwide.

In Manitoba, the only waterways covered by the new Navigation Protection Act would be Lake Winnipeg, Lake Manitoba, Lake Winnipegosis, the Winnipeg River, the Red River and the Assiniboine River.

"On our environment, across Canada, this could hardly be a bigger blow," said Eric Reder, Manitoba campaign director for the Wilderness Committee.

The current act applies to almost every body of water in Canada.

The Conservatives say the act needs to be changed because it is an impediment to development. Transport Minister Denis Lebel, grilled about the changes Tuesday, said provinces and municipalities have asked Ottawa to cut the red tape of the Navigable Waters Protection Act for years.

"The act has created a bureaucratic black hole, holding up simple projects that do not impede navigation," he said. "Under our plan, only projects likely to offset navigation require approval to changes about navigation."

Only proposed projects for the waterways listed in the new act will require ministerial approval once the budget bill passes.

All others can proceed without limitation although the government notes those proposing to build on a waterway that is not listed in the act can voluntarily ask for approval.

Manitoba Conservative MP Merv Tweed told the House of Commons small governments in particular were "just being crushed by the burden of paperwork" associated with the act. He said it took one municipality in his riding five years just to replace a damaged rock bridge, and it was only when the flood of 2011 hit "when pretty much no rules applied" that it finally managed to get it done.

However, opposition parties claim the government is using the act for partisan gain, after an analysis found almost nine in 10 of the waterways that remain protected are in Conservative ridings.

"Canadians deserve better than Conservative preferential treatment of their friends," said NDP MP Megan Leslie. "Why are the Conservatives making environmental protection a privilege of the few?"

The government contends the act was never about the environment but only about navigation.

Reder, however, said over time, the act did become about environmental protection because it had provisions that automatically triggered a review under the Canadian Environmental Assessment Act.

He said major projects will likely still be reviewed but smaller projects, such as those for expanding logging and mining operations, could fly under the radar.

Manitoba Liberal Leader Jon Gerrard called on Premier Greg Selinger to lodge an official protest over the changes or introduce provincial protections to replace the federal law.

A spokeswoman for Conservation Minister Gord Mackintosh said many of the waterways affected by the amendments to the federal law are covered under Manitoba's Environment Act or Water Rights Act, but the province will study the proposed federal changes to see if there will be any negative impact on Manitoba's navigable waters.