In a letter to Harper sent Thursday, the 625 scientists express concern the federal government is set to remove habitat protections from the Fisheries Act.
"This would be a most unwise action, which would jeopardize many important fish stocks and the lakes, estuaries and rivers that support them," the letter states.
"We urge you to abandon this initiative."
The changes, expected to be signalled as a streamlining of environmental assessments in next week's budget, would reflect the Conservative government's push to break down barriers to development.
Last week, a leaked draft showed Ottawa wants to remove habitat provisions from the act, raising concerns that would essentially dilute government oversight in the face of industrial development.
"If that's even close to what they're going to announce, you'll see some of the senior scientists in this country joining the green groups and native people on the picket lines," said David Schindler, ecology professor at the University of Alberta.
Speaking from Edmonton, the internationally noted ecologist and former longtime civil servant said the "pro-development" Conservative government seems determined to ride roughshod over environmental protections.
"I'm told that we can expect a gutting of every environmental law if this government gets its way," Schindler said.
The scientists, including many of Canada's most senior ecologists and aquatic scientists, take a particularly jaundiced view of the government's apparent wish to apply protection of fish habitat only to "fisheries of economic, cultural and ecological value."
"This makes no sense," they write. "All species are of ecological value."
In Toronto for a Great Lakes cleanup announcement Thursday, Environment Minister Peter Kent called the concerns about the "still unspecified changes" legitimate.
At the same time, Kent urged the letter writers to wait for Fisheries Minister Keith Ashfield to present the changes rather than react to "exaggerated" speculation.
"The Environmental Assessment Act does (apply to) fish habitat," Kent said.
"I can assure you: There will be no short cuts or negative changes to enforcement or implementation of (the act)."
Ashfield has said no decisions have been made, but said current policies overreach and are under review to better reflect "the priorities" of Canadians. His office has given no details but called "unfocused and indiscriminate" rules a "systemic" problem.
"We are reviewing policies to ensure they do not go beyond their intended conservation goals," Ashfield's spokeswoman Erin Filliter said Thursday.
Schindler said the Fisheries Act is considered to be Canada's strongest environmental-protection measure and expressed dismay it could be undermined.
"The wording of the Fisheries Act is just fine the way it is, if they would simply enforce it," Schindler said.
The letter also warned that weakening habitat protections would make Canada "look irresponsible internationally."
Green party Leader Elizabeth May accused the government of stepping up "its war" on environmental regulations.
"There is a definite pattern emerging," May said in Ottawa.
"Whatever restraints may exist for industry to go full steam ahead on whatever project they want are now being systematically dismantled."
Removing habitat protections in the act would be a "death blow," she said.
On Monday, the Canadian Society for Ecology and Evolution, an organization of more than 1,000 ecologists and evolutionary biologists across Canada, also said they opposed weakening the Fisheries Act.