BALTIMORE -- The Maryland Port Commission, beginning the slow process of paying for the state's new Seagirt Marine Terminal, has agreed to pay a bargain first-year rent of $3.5 million for the facility.

The Maryland Transportation Authority, another agency that builds and operates the state's bridges and tunnels, is the banker and landlord of the property because it put up about $240 million to build Seagirt.

The authority intends to make some money on its investment in the marine terminal and its adjoining rail yard. However, at a rate of $3.5 million a year, it would take the port 71 years to pay off the principal.

Future payments will be negotiated by the two state agencies. A tentative, two-year agreement between the two was approved Monday by the Maryland Port Commission, which oversees the Maryland Port Administration. The deal will go before the transportation authority today and will be effective for the fiscal year that began July 1.

"I think it's fair to both sides," said Richard Trainor, who, as transportation secretary, is chairman of the transportation authority and the port commission.

He said the port administration will eventually pay off the debt, and provide some modest return on investment for the transportation authority. But it may take 25 to 30 years, depending on how well Seagirt attracts customers and what prices the state can charge them.

There is pressure to keep rates low. Seagirt's opening is more than a year behind schedule, and only one ship line has signed a lease. The state hopes the first ship will call at Seagirt this month or next.

Trainor said the commission does not intend to charge below-cost rates at Seagirt. However, he added, "The key is filling it up with customers."

The transportation authority, he said, "Understands our position. The money they have is public money and it is an investment for public benefit."

The agreement between the agencies calls for the rent to be renegotiated in the second year, after which the whole agreement is up for renegotiation.

Even with the low initial rent, there is no guarantee that the port administration will make money at Seagirt from the fees charged ship lines and other terminal users. The port administration posted a nearly $4 million operating loss in fiscal 1989 and anticipates another loss in the just-completed fiscal 1990.

Some legislators have expressed concern that Seagirt will merely draw cargo from other terminals, resulting in higher operating costs and lower rent and revenue. But port officials hope Seagirt will reinvigorate the Port of Baltimore, bringing back business lost to competing waterfronts and reversing the port agency's financial troubles.