The interstate Commerce Commission approved a plan yesterday that will allow Auto-Train Corp. to issue a $3 million note, improving its chances of recovering from financial difficulties.

But the commission's approval of the financing plan is dependent on Auto-Train agreeing to repay thousands of dollars to customers who have not been reimbursed after cancelling reservations.

The action follows by one day a formal complaint by the U.S. Office of Consumer Affairs, which urged the commission to consider the refund problem carefully.

Under the ICC proposal, Auto-Train must repay all canceled advance sales older than 90 days by Jan. 15, 1980, older than 60 days by Feb. 15, 1980, and older than 30 days by March 15, 1980.

In addition, the ICC asked Auto-Train to set up an escrow account for future refunds. That account will consist of one percent of the Washington-based company's gross passenger revenues beginning on Jan. 2 and would be increased by $500,000 on March 15.

The authorization for the note is not effective until Auto-Train agrees to the ICC refund proposal.

The 13 percent note, issued to Paul Revere Life Insurance Co., is to be repaid by April 1, 1984. Proceeds fro the note will be used to repay American Security Bank for other Auto-Train debts.

"New interest in the use of applicant's (Auto-Train's) services has been generated by the energy problems presently affecting the country, and this increase should also generate additional funds which will facilitate the elimination of a refund backlog," the ICC said, in a unanimous opinion.