This Western Painted Turtle is one of about 100 living in Burnaby Lake and holding up a $20-million dredging project. (CBC)

The City of Burnaby says it may sue the B.C. provincial government for the last-minute denial of permits needed to dredge Burnaby Lake — but the province says it's just trying to protect an endangered turtle.

Burnaby has been planning to dredge the 1.5-kilometre-long body of water for more than five years, trying to remove mud and plants like water lilies that have slowly been filling the lake, according to city officials.

Work was to begin Wednesday on the $20-million project.

"I'm shocked, I'm appalled, I can't believe that at this late date the [Environment] ministry is throwing more obstacles in the way of dredging the lake," Mayor Derek Corrigan told CBC News Tuesday.

"This is likely going to cost the province and the city millions of dollars if we can't go ahead with this project," Corrigan said.

Dredging some 250,000 cubic metres of sediment would increase the lake's usable surface area, allowing the city once again to host major rowing competitions.

'This is a really important population to keep around'—Biologist Vanessa Kilburn

Standing in the city's way is the endangered Western Painted Turtle. Burnaby Lake is the only place in the Lower Mainland with healthy population, according to an expert.

"If there's a chance for recovery of this species in the Lower Mainland [and] Fraser Valley, it's going to come from this population," said biologist Vanessa Kilburn.

"This is a really important population to keep around," said Kilburn, who is part of the Western Painted Turtle Recovery Team, a government-mandated group organized by the B.C. Ministry of Environment, and Environment Canada.

Dredging at this time of year, as the turtles are starting to hibernate, could kill the lake's population off, said Kilburn.

"The dredging machines chop up the sediment on the bottom and spit it out the back," Kilburn said. "We wouldn't even have known if the turtles were killed."

The project passed an environmental assessment that included plans to protect the turtles, Corrigan said.

When it became apparent this week, however, that it was too late in the year to trap and move the turtles successfully, the final permit required for work to begin was denied, according to an environment ministry spokesperson.