As a fleet of five boats left port early on Monday, whalers, their families and local officials in two major whaling towns, Shimonoseki in southwestern Japan and Kushiro in the north, celebrated the fresh start, hoping for their safe return and a good catch.
Two minke whales were brought back to Kushiro later on Monday.
A crane lifted them and slowly placed them on the back of a truck to be taken to a portside factory for processing.
Workers in blue plastic overalls poured sake from paper cups onto the first whale to express thanks and celebrate the first catch.
Fisheries Agency officials said the whale meat would be auctioned at a local fish market on Thursday and later hit stores, mainly in the region but possibly in Tokyo.
"We hope commercial whaling will be on track as soon as possible, contribute to local prosperity and carry on Japan's rich whale culture to the next generation," Deputy Chief Cabinet Secretary Yasutoshi Nishimura told reporters in Tokyo.
Whale meat was an affordable source of protein during the lean times after World War II, with annual consumption peaking at 223,000 tonnes in 1962. But whale was quickly replaced by other meats.
The supply of whale meat fell to 6,000 tonnes in 1986, the year before the moratorium on commercial whaling imposed by the IWC banned the hunting of several whale species.
Under its research whaling, which was criticised as a cover for commercial hunts because the meat was sold on the market, Japan caught as many as 1,200 whales a year.
It drastically cut back its catch in recent years after international protests escalated and whale meat consumption slumped at home.
Today, about 4,000-5,000 tonnes are supplied in Japan annually, or 30-40 grammes of whale meat per person a year, Fisheries Agency officials say.
The research whaling programme lost money for years - 1.6 billion yen ($15m) in the last year alone.