In a letter published online Thursday in the journal "Science," the scientists from Simon Fraser University criticize cutbacks at eco-toxicology labs and an aquatic research facility and changes to the act itself, saying the government's rational for making the changes is not supported by fact.
The changes are part of the omnibus budget bill known as Bill C-38, which passed third reading in Parliament earlier this week but has not yet become law.
The Department of Fisheries and Oceans did not respond to a request for comment on the letter.
"Where it seems that the evidence doesn't support the claims, it's important that people look at that and make the leaders aware of that, and continue to call out that we do value evidence and we do value effective management of the country," said Brett Favaro, a PhD student at the university.
"So that's where this really comes from is looking at the data and making sure we are making the best decisions based on the data."
According to the bill currently before the Senate, the amended act would only apply to major waterways and only to prohibit "serious harm" to a commercial, recreational or aboriginal fishery.
"Serious harm" is defined as death or permanent damage to habitat.
The changes would also give the federal government more leeway to allow exceptions.
The Conservative government has argued the legislation has been applied indiscriminately against ditches and other structures unlikely to bear fish and as a result has interfered with landowners and farmers, write Favaro, and SFU biology professors John Reynolds and Isabelle Cote, citing Parliamentary debates.
The government has also argued that removing habitat protection would enable Canadians to undertake activities on their properties without obtrusive interference, the scientists add.
But they write that the reasons for making those changes are not supported by evidence.
In fact, the scientists write that between 2006 and 2011, only one proposal reviewed by the federal environmental assessment process was rejected because of potential destruction to fish habitat.
And of 1,283 convictions under the Fisheries Act announced in media releases between 2007 and 2011, only 21 pertained to the destruction of fish habitat, write the scientists.
"Ours is the first, to my knowledge, quantitative assessment, where we actually looked at the data and figured out what they're saying," said Favaro.
He said he hopes politicians will review the bill because of public concern.
During the past 100 years, the country has lost about one-seventh of its wetlands, and it continues to lose them, a fact that will eventually lead to the loss of fish, he added.
The letter by the three scientists will also appear in the hardcopy edition of "Science" on Friday.
Four former fisheries minister — two Conservative and two Liberal — said in an open letter last month they don't believe the government of Stephen Harper has given a good explanation for including environmental provisions in a budget bill.
"We find it troubling that the government is proposing to amend the Fisheries Act via omnibus budget legislation in a manner that we believe will inevitably reduce and weaken the habitat protection provisions," wrote Tom Siddon, David Anderson, John Fraser and Herb Dhaliwal.
All former ministers are from British Columbia.
Recently, Canada's only marine-mammal toxicologist, Peter Ross, announced he'd be losing his job at the Institute of Ocean Sciences on Vancouver Island because of federal budget cuts at Fisheries and Oceans.
The Fiseries Department will be slashing about 400 positions from its 11,000-strong workforce.