The A.F.L.-C.I.O. and other groups filed a complaint with the Biden administration on Monday over claims of labor violations at a group of auto parts factories in Mexico, a move that will pose an early test of the new North American trade deal and its labor protections.

The complaint focuses on the Tridonex auto parts factories in the city of Matamoros, just across the border from Brownsville, Texas. The A.F.L.-C.I.O. said workers there had been harassed and fired over their efforts to organize with an independent union, SNITIS, in place of a company-controlled union. Susana Prieto Terrazas, a Mexican labor lawyer and SNITIS leader, was arrested and jailed last year in an episode that received significant attention.

The trade deal, the United States-Mexico-Canada Agreement, was negotiated by the Trump administration to replace the North American Free Trade Agreement and took effect last summer. While it was negotiated by a Republican administration, the deal had significant input from congressional Democrats, who controlled the House and who insisted on tougher labor and environmental standards in order to vote in favor of the pact, which needed approval from Congress.

The trade pact required Mexico to make sweeping changes to its labor system, where sham collective bargaining agreements known as protection contracts, which are imposed without the involvement of employees and lock in low wages, have been prevalent.

The complaint is being brought under a novel “rapid response” mechanism in the trade deal that allows for complaints about labor violations to be brought against an individual factory and for penalties to be applied to that factory. The complaint was filed by the A.F.L.-C.I.O., the Service Employees International Union, SNITIS and Public Citizen’s Global Trade Watch.

The trade deal seeks to improve labor conditions and pay for workers in Mexico, which proponents say would benefit American workers by deterring factory owners from moving their operations to Mexico from the United States in search of cheaper labor. Enforcement of the pact is one of the main trade challenges facing the Biden administration.