A special presidential panel, working to head off a threatened nationwide rail strike, yesterday recommended a 21 percent pay increase over five years for union workers in the industry and proposed that they begin paying part of their health care costs.

The recommendation by the three-man Presidential Emergency Board starts a 30-day "cooling off" period that expires at midnight Feb. 14. If no agreement is reached by then, nearly 200,000 workers in 10 unions will be free to shut down railroad freight service nationally unless Congress intervenes with emergency legislation.

There were indications, however, that the unions would not strike while the United States is at war in the Persian Gulf. "We're not going to be unpatriotic and shut down the railroads ... ," said Richard Kilroy, president of the Transportation Communications Union and a leader of the rail unions.

Charles I. Hopkins Jr., chief negotiator for the railroads, said the board's recommendations go "too far on wages and not nearly far enough on work-rule relief." The industry has proposed a wage freeze, coupled with an easing of union work rules and relief from health care costs.

Richard Kilroy, a key union leader and president of the Transportation Communications Union, was optimistic yesterday that the board report could serve as the basis for a negotiated settlement before the strike deadline.

Kilroy said he thought the other unions would go along with both the wage and the health care proposals if the railroads would back away from their demands for work-rule concessions that would allow more flexibility in repairs and operations.

Although the pay increases proposed by the board total 21 percent plus a $2,000 signing bonus for most workers at the start of the contract, there is less than meets the eye for the average worker. Under the board proposal, union workers would receive a 3 percent general wage increase July 1, 1991, another 3 percent in July 1993 and a 4 percent general increase in July 1994. The rest of the money would be in the form of lump-sum payments that would not count for purposes of calculating fringe benefits such as pensions.