The department said it's launching an effort to relocate the species before construction of the Detroit River International Crossing in west Windsor ramps up next summer.
It said at least 277 Dense Blazing Star plants and 180 Willow Leaf Aster ramets will be moved between November 2012 and May 2013.
It said the plants will be relocated to the eastern side of Lake St. Clair, near Chatham-Kent.
The plants in question on the site of the proposed customs and toll plaza.
According to Windsor Gateway Project spokesperson Mark Butler, Transport Canada will relocate all species at risk found on the plaza site in order to protect their survival.
Environment Canada issued Species at Risk Act and Canadian Wildlife Area permits in June 2012 to allow the removal and transplanting of several hundred Dense Blazing Stars and Willow Leaf Asters, as well as approximately 3804 square metres of associated Tallgrass Prairie vegetation. It will all be moved to the Lake St. Clair National Wildlife Area near Chatham, Ont.
"The cost of the contract is not known as the contract has not yet been awarded," Butler wrote in an email to CBC News. "The Government of Canada takes its environmental responsibilities very seriously and has and will continue to adhere to all requirements under the Canadian Environmental Assessment Act for the Detroit River International Crossing project."
Earlier this month, the Harper government announced in its latest omnibus bill it will exempt the new Windsor-Detroit bridge from major Canadian environmental laws.
The Conservatives introduced the Bridge to Strengthen Trade Act as a part of the omnibus budget bill tabled in the House of Commons.
Once passed, bridge construction would be immune to laws governing permits, approvals and authorizations, including the Environmental Assessment Act and the Species at Risk Act.
The province, meanwhile, has already spent time and money relocating and protecting snakes, the Dense Blazing Star, Common Hoptree, Willowleaf Aster, Dwarf Hackberry and Kentucky Coffee Tree in the construction of the $1.4-billion Windsor-Essex Parkway which will eventually connect Highway 401 with the new bridge.