The whaling ships headed home from the Antarctic Ocean this week with 266 minke whales and one fin whale, said the agency on Friday.
This is far short of the quota of about 900 set when they began the hunt in December 2011.
Japan's fleet sails south to the Antarctic in the autumn each year, returning the following spring.
There has been a ban on commercial whaling for 25 years, but Japan catches about 1,000 whales each year in what it says is a scientific research programme.
Critics say it is commercial whaling in another guise.
Anti-whaling group Sea Shepherd which follows the Japanese fleet south every year in a bid to disrupt its hunt announced on its website on Thursday that the whalers had left the Southern Ocean.
There have been several clashes between the activists and whalers in the past months.
In January, three activists said they suffered cuts and bruises after clashing with a Japanese ship, the Yushin Maru No 2, about 300 miles north of Mawson Peninsula off the coast of Antarctica.
The Institute of Cetacean Research (ICR), which sponsors Japan's whaling activities, said the activists were trying to ''sabotage'' the Yushin Maru, throwing ropes with hooks attached and also hurling glass bottles of paint.
The vessel was one of the security ships escorting the whaling fleet.
The week before the incident, Japan handed three anti-whaling activists who had boarded a whaling support ship back to Australian authorities.
"The catch was smaller than planned due to factors including weather conditions and sabotage acts by activists," AFP news agency quoted an agency official said. "There were definitely sabotage campaigns behind the figure."
The agency said the fleet had departed "as scheduled".