Trans World Airlines will pay an estimated $629,000 in refunds, plus interest, to passengers it overcharged during a five-day period last September, the Civil Aeronautics Board announced yesterday.

In an agreement worked out with the CAB, TWA also agreed to pay up to $80,000 in civil penalties, without admitting any violation of federal law.

The agreement stems from an investigation initiated by the board's Bureau of Consumer Protection.

On Aug. 31, the CAB approved a new, increased domestic fare level for airlines effective Sept. 1. TWA began charging the higher fares Sept. 1, but didn't file a tariff reflecting the higher fare rates until Sept. 5.

Federal law prohibits carriers from charging fares different from those contained in the tariff. The agreement requires TWA to find all passengers charged fares higher than those in TWA's tariffs from Sept. 1 to 5, and pay them the excess charged plus interest at a rate of 1.5 percent per month.

TWA estimates 33,480 passengers were overcharged during the five-day period, according to documents filed in the investigation.

If more than 15 percent of the passengers cannot be found, TWA will hire an independent auditor to verify it took all reasonable steps to carry out its refund program.

The agreement also requires TWA to pay $50,000 in civil penalties immediately, and additional amounts of $10,000 each September for the next three years if the refund program hasn't been completed by that time.