A Japanese whaling ship has returned home to the country's southwest after almost meeting its annual quota, ending its first commercial whaling season in 31 years.

Operator Kyodo Senpaku Co. said its main factory ship Nisshin Maru returned to its home port of Shimonoseki after catching 223 whales during its three-month expedition off the Japanese coast.

Nisshin Maru's two support ships, Yushin Maru and No. 3 Yushin Maru, also returned to their home ports.

AAP

Japan resumed commercial whaling on 1 July after leaving the International Whaling Commission, promising that the whalers would stay within the country's exclusive economic waters.

Japan had conducted research hunts for 31 years in the Antarctic and the Northwest Pacific that conservationists criticised as a cover for commercial hunts banned by the IWC.

Kyodo Senpaku President Eiji Mori praised the whalers for returning with "better than expected" results despite earlier uncertainty because of their lack of experience in the area.

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"We were worried if we could catch any, but they did a great job," Mori said. "We will examine the results closely and make a plan for the next season."

Of the quota of 232 whales allocated to the main fleet, they caught 187 Bryde's, 25 sei and 11 minke whales, only nine minke whales short of the cap.

The fleet brought back an estimated 1300 tonnes of frozen whale meat from the catch, down 600 tonnes from last year's Antarctic hunts.

READ MORE Japan to resume commercial whaling for first time in three decades despite outcry

Separately, whalers operating smaller scale hunts in waters just off Japan's northeastern coasts were given a seasonal quota of 33 minke whales. Days after the resumption, their fleet of five small boats returned with two minke whales, whose fresh meat fetched as much as 15,000 yen ($A200) per kilogram at a local fish market auction celebrating the first commercial hunt in three decades.

While opponents condemn Japan's commercial whaling, others question if the embattled whaling program can survive changing times and tastes.

Whale meat was an affordable source of protein during the lean times after World War II, with annual consumption peaking at 208,000 tonnes in 1962, but whale was quickly replaced by other meats.

Today, annual consumption was down to about 3600 to 4500 tonnes, according to the Fisheries Agency.