The Canadian Centre for Policy Alternatives says the proposed Comprehensive Economic and Trade Agreement could cost Manitoba up to 3,800 jobs.
The think-tank, which says it focuses on issues of social and economic justice, argues the deal could wipe out rules in provincial and municipal government contracts that set quotas for local hiring and purchasing.
The report also suggests any deal could add to an existing trade imbalance, which sees Manitoba export mostly raw material to Europe while importing finished products.
The federal government has predicted a much more positive outcome.
It says Manitoba would gain through lower tariffs on agricultural products, electronics and other goods.
Across Canada, the government has predicted 80,000 jobs could be created. But the authors of the report say leaked details of the negotiations suggest otherwise.
"The drafts ... indicate that provincial governments and Crown corporations will be restricted in the use of their purchasing power to ensure that local and provincial firms are allocated a portion of government goods and services procurement," John Jacobs and Lynn Fernandez write in the report released to be release Thursday.
They say that could be especially problematic in northern Manitoba communities where a share of mining and hydro projects are set aside for local firms.
The Canadian Centre for Policy Alternatives issued a similar report for the Atlantic provinces last month which said a trade deal could wipe out protections for fishery jobs.
The federal government disputed those findings. It said rules on ownership of fishing companies and who can have access to inshore fisheries would remain. It also said European tariffs on Canadian seafood, as high as 25 per cent, would be eliminated.
Canadian and European negotiators had hoped to reach an agreement by the end of 2012, but there were disagreements over barriers on beef, automobiles and other items.