The incident happened in the Antarctic Ocean last month.
The Sea Shepherd Conservation Society's Pete Bethune has been held on board the Shonan Maru No. 2 since the incident, Kyodo News reported. The ship is due to arrive in Tokyo Friday.
Kyodo said after the vessel arrives the Coast Guard plans to have the activist handed over for questioning.
Bethune was the captain of the Sea Shepherd vessel Ady Gil. The vessel was disabled after it clashed with the Japanese vessel in Antarctic waters in January, the report said.
Bethune traveled by jet ski from another protest vessel to present a protest letter to the captain of the Shonan Maru No. 2. The letter blamed the Japanese ship for the collision.
In Japan, conviction of trespassing on a vessel can carries a penalty of up to three years in prison or a maximum fine of 100,000 yen ($1,106), but Kyodo said such an offense usually doesn't result in an arrest.