The NFL Players Association announced today it has filed a grievance challenging a key provision in the free-agent system contained in the union's collective-bargaining agreement with the league.

If an arbitrator rules in the union's favor, the Redskins, for example, could lose running back Mike Thomas after the 1979 season and receive no compensation if he signed with another NFL team.

"We are talking about a guy who has played out his option but who has failed to generate an offer from another team by the April 15 deadline," said Dick Berthelsen, the union's staff counsel.

"Let's take Mike Thomas (who played out his option last season) as an example. If he does not get an offer by then (April 15, 1979), the current rule says the Redskins can compel him to play for them again. They must take him by June 1, at which time he has a choice of playing for them at a 10 percent increase over last year's contract, or he can accept the last best written offer they made him prior to his becoming a free agent.

"If he decided to play that next year (1979) under those terms, that's when the dispute arises. If he has to play that extra year, we contend he should be a totally free agent the following year, with no restriction on who can sign him, and no draft choices awarded as compensation. The league says no, that he still must go back into the system. That's what we want decided."

Berthelson said the case will go directly to James Scearce, the arbitrator agreed upon by both management and the union in their negotiations, and he said he hoped for a decision within the next month.

In other developments:

Executive Director Ed Garvey said the union was still actively considering bargaining for a specific wage scale based on percentages of gross revenues of NFL franchises and years of service in the league when the current contract expires in 1982.

NFL assistant coaches have approached the players' association about the possibility of organizing into a union and negotiating for contracts. Garvey said 80 assistant coaches of 216 queried have responded favorably, and if that number reaches 100, "we'll definitely be interested in getting involved." NFL trainers also may come under the protection of an assistat coaches' union, he said.