ALBANY – The largest state government workers union Monday filed two federal lawsuits against the State Thruway Authority, alleging the agency’s April layoffs illegally targeted only unionized workers.

The Civil Service Employees Association brought its action on behalf of 99 CSEA members who were either fired, forced into retirement or took lower-paying jobs at the agency.

“The fact that only union members were targeted proves the layoffs were meant to punish them. If the layoffs were truly necessary, wouldn’t it make sense to get rid of at least one highly paid manager or appointee?” asked CSEA President Danny Donohue.

The agency in early April terminated more than 200 workers statewide, including office staff, toll collectors and maintenance staff.

Most of those affected were members of Teamsters Local 72, which has already filed an improper-practice charge over the layoffs.

Dan Weiller, spokesman for the Thruway Authority, said, “We have not seen any detail or documentation regarding a possible lawsuit by CSEA, and we do not comment on matters under litigation.”

The CSEA filed its lawsuit on behalf of 60 affected members at the Thruway and 39 at the state’s canal corporation, which the Thruway Authority runs. The lawsuits allege that Joseph Bress, the agency’s chief contract negotiator, last December began threatening the CSEA with layoffs unless savings were found at the agency. The union’s contract expired in June 2012.

A week before the layoffs, the CSEA lawsuit says, the Thruway Authority’s board was told the agency was in “solid” financial shape.

The federal lawsuit alleges that the workers’ constitutional rights to freedom of speech, freedom of association, due process and equal protection of the law were violated.

The layoffs were announced a month after the Thruway Authority, under intense pressure from business organizations, abandoned a plan to raise $90 million a year in new tolls on trucks.