Five boats set sail this morning following the country's decision to withdraw from the International Whaling Commission (IWC) last year.
Until today, Japan had hunted whales in Antarctic waters saying the expeditions were to carry out scientific research, which were permitted due to a loophole in IWC rules which ban commercial hunts.
Now it will hunt whales in its own waters for commercial use, including as meat.
The decision to quit the IWC was celebrated by whaling communities but criticised by environmental groups and other nations which support the ban.
Japan has long argued that whaling is an important tradition, with whale meat providing a key source of protein as the nation recovered from the second world war. However, in recent times demand for whale meat has fallen.
The Australian Marine Conservation Society (AMCS) called commercial whaling an 'outdated and cruel industry selling a product to a market that has all but disappeared.'
