Auto-Train Corp. announced yesterday it will no longer accept travel agents' cetrificates for tickets on its trains, because an estimated $250,000 worth of the certificates cannot be accounted for.

Passengers should not buy or accept any of the certificates because they may not be valid, said a spokesman for Auto-Train, which last month filed for reorganization in bankruptcy.

The warning does not apply to regular Auto-Train tickets, most of which are purchased directly from the railroad.

Earlier this week Auto-Train bankruptcy trustee Murray Drabkin obtained a court order instructing a New York firm. Trafalger Capital Corp., to account for the certificates that were issued to it by Auto-Train last summer.

In July, Auto-Train signed an agreement for marketing and advertising services with Trafalger. Because Auto-Train was short of cash, Trafalger agreed to accept $1 million in credit for travel on the train.

But in the report to Drabkin this week, Trafalger said it had prepared $2 million worth of certificates and had $1.7 million on hand. About $60,000 worth of the certificates have already been used.

The remainder have not been accounted for, and the bankruptcy trustee reportedly so far has not been able to determine what services Trafalger had provided for Auto-Train and how much money the railroad owes.