Some Japanese media have said the announcement is being delayed to avoid trouble at the G20 meeting, but industry experts deny this.
While the resumption of commercial whaling is condemned by many conservation groups, others see it as a face-saving way to let the government's embattled and expensive whaling programme gradually succumb to changing times and tastes.
As with other types of whales, including orca, sub-populations of the same species can develop highly distinct behaviour patterns, which has led some biologists to describe these differences as "cultural".
Its last commercial hunt was in 1986, but Japan has never really stopped whaling - it has been conducting instead what it says are research missions which catch hundreds of whales annually. "People have hunted whales for more than 400 years in my home town".
Darren Kindleysides, AMCS chief executive officer, said: "Whaling is a dying industry - it is an outdated and cruel industry selling a product to a market that has all but disappeared".
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The research whaling program lost money for years - 1.6 billion yen ($15 million) in the last year alone.
The country's Fisheries Agency said the catch quota for 2019, which will be limited to whales in its EEZs, was set at 227 whales. A number of coastal communities in Japan have indeed hunted whales for centuries but consumption only became widespread after World War Two when other food was scarce.
Commercial whaling began in the 1800s and nearly drove whales to extinction. By afternoon, one ship had returned with a roughly 8m-long minke whale. Nevertheless, Iceland and Norway catch whales for commercial purposes, even though Iceland does not want to hunt whales this summer. Altogether, they will catch 52 minkes, 150 Bryde's and 25 sei whales through December 31.
But with the official restart of commercial whaling, Japanese boats will now hunt in the country's territorial waters.
Another ship caught a whale, but the vessel had not returned by evening and no further details were available.
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Commercial whaling in Japan has returned after the country lifted its 31-year-long ban.
The agency said Monday annual whale meat supply from commercial whaling is expected to be lower than that from scientific whaling.
"I don't think young people know how to cook and eat whale meat anymore".
The sei - at 20 metres (645 feet), the biggest of whales after the blue and the fin - was the main target of Japan's ostensibly "scientific" whaling from the early 2000s until 2017.
"What we are seeing is the beginning of the end of Japanese whaling", said Patrick Ramage, director of marine conservation at the International Fund for Animal Welfare. With this announcement Japan has declared themselves as a pirate whaling nation.
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"My heart is full of hope", added Kai, who belongs to a fisheries cooperative in Taiji in Wakayama prefecture, an area known for both whale and dolphin hunting.