Seatrain Lines Inc., the big shipping company that dropped its North Atlantic shipping in September, reported today that it lost $4.9 million during the three months ended Sept. 30.

The company attributed most of its losses to the troubled North Atlantic routes but said it also lost money in its Middle East and Mediterranean shipping. Because of a decline in trade, there is widespread rate-cutting among shippers anxious for business.

Seatrain has been in financial difficulty for several years. The company shut down its shipbuilding facility at the old Brooklyn Navy yard in 1979 after 10 years of trying to make a go of it.

In its 1980 fiscal year, which ended June 30, Seatrain lost about $35 million on revenues of $1.3 billion. In 1979 the New Jersey-based concern lost $36 million on revenues of $789.9 million. The losses in 1979 were attributable to the shutdown of the shipbuilding facility.

Seatrain said today that in its first quarter it had revenues of $316.2 million compared with $262.2 million in the first quarter of its 1980 fiscal year. Last year, however, Seatrain had a net income of $2.4 million compared with this year's $4.9 million loss.

Chase Manhattan Bank, the company's prime lender, has agreed to permit Seatrain to defer payment of interest on loans outstanding because of the shipping company's cash problems.

Although Seatrain is best-known for the operation and chartering of ocean-going vessels, the main source of its revenue is an oil refinery in Abilene, Tex.

A spokesman said that the oil refinery contributed $194.1 million in income during the first three months, while its liner service contributed $89.4 million and the vessel-chartering operation had $32.7 million in revenues.

When Seatrain dropped out of the North Atlantic on Sept. 4, it turned over six chartered container ships and 7,000 containers to Trans Freight Lines Inc., a subsidiary of the Australian conglomerate Thomas Nationwide Transport Ltd., for $15 million in cash and $13.5 million in notes. The company realized a net gain of $7 million on the sale.