Under the proposal, released Thursday by the Fisheries Resource Conservation Council, about 73,000 animals would be killed in the first year, and another 70,000 would be taken over the next four years.
Council chairman Gerard Chidley said scientific evidence suggests grey seals are the most likely cause of the slow recovery of groundfish stocks, including cod, in a vast area that stretches from Quebec's Gaspe Peninsula to the east side of Cape Breton.
He said the proposed slaughter is an experiment aimed at determining if that hypothesis is valid.
"The lack of recovery for groundfish stocks has created a high level of frustration in the industry and led to severe criticism of the government of Canada for not rebuilding the stocks," Chidley told a news conference.
"The council believes that evidence supporting this idea is sufficiently strong ... that it is now time to proceed as soon as possible with a targeted seal removal."
The recommendation mirrors a proposal released in March by the Canadian Science Advisory Secretariat, which works for the federal Fisheries Department. The council consists of 12 members appointed by the minister of fisheries and oceans to provide advice.
It's now up to Fisheries Minister Keith Ashfield to decide whether the proposal is a good idea.
The secretariat says there are between 330,000 and 410,000 grey seals living off the Atlantic coast -- a 30-fold increase since the 1960s. Most of Canada's grey seals -- at least 260,0000 -- live part time on Sable Island, a spit of land about 160 kilometres southeast of Nova Scotia.
Representatives from Atlantic Canada's fishing industry have long claimed that hungry seals have been thwarting the recovery of groundfish stocks, which collapsed in the early 1990s after decades of overfishing.
Animal welfare activists criticized the science that's used to justify a cull.
"They're taking a political decision to cull seals and trying to couch it in some kind of scientific language and portray it as an experiment," said Sheryl Fink, seals campaign director for the International Fund for Animal Welfare.
"They don't have a clear grasp of what science can and cannot do. ... From a scientific point of view, this isn't going to tell us anything about the relationship between seals and cod. It's dishonest to portray it as an experiment."
Fink said that even if the stocks were to recover after the five-year experiment, there would be no scientific evidence to establish a cause-and effect relationship because there are too many factors influencing the groundfish population.
"It's a politically popular thing to do," she said. "We've been using seals as scapegoats for fisheries mismanagement for years."
Chidley bristled at the suggestion that the council's advice to the federal government is motivated by politics.
"This reduction of the herd in the southern Gulf is scientifically based," he said.
Still, the council's report says there are risks associated with the experiment.
"Because groundfish and seal populations do not interact in isolation ... it is likely that large experimental reductions in seal abundance will produce unexpected effects on other species," the report says.
In fact, an earlier report from the federal science secretariat concluded that there are such large gaps in research on the problem that a large-scale cull could lead to wiping out cod in the Gulf.
As well, the council is worried about how the rest of the world will perceive the cull.
"We are subject to intense international scrutiny that has the potential to put established markets for Canadian seafood products at serious risk," the council said.
Seal hunters typically slaughter about 1,000 grey seals in the Gulf every year, even though the allowable catch is about 50,000. The annual Canadian commercial seal hunt has long focused on the far more numerous harp seals, which are estimated to number about nine million off the East Coast.
The council's report notes there is no real market to sell grey seal products.
"In the short term of the initial experiment, large numbers of seals must be killed even in the absence of commercial gain."