One crew member was wounded when a Russian patrol boat hit one of the ships, Anatoly Prokopev, spokesman for the border guards in Moscow, said during a telephone interview.
Russian border guards have complained about Japanese poaching for over a year now.
Prokopev said there had been 50 illegal entries into Russian territorial waters since Aug. 6.
Monday's shooting could be repeated if poachers attempt to enter Russian waters again, he told The Moscow Times.
The incident may rekindle a territorial dispute between Russia and Japan because it took place near four Kuril islands that are claimed by Tokyo but have been controlled by Moscow ever since World War II.
Prokopev said the patrol attacked when the unmarked ships ignored repeated warnings and warning shots and tried to flee Russian waters.
The damaged boat was towed to shore.
The crew of four members was detained.
The other ship escaped.
According to Prokopev, the crew admitted guilt and were awaiting a formal arrest.
Japanese Embassy spokesman Yoshitaka Akimoto said Japan had demanded an explanation from the Foreign Ministry.
Additionally, Akimoto commented that it was "too early to state our position because we don't know the details."
"If this incident happened in our sovereign territory, including the territorial waters surrounding the four islands, it is totally unacceptable that the Russians attacked our official boat," Akimoto said in a telephone interview Monday.
A Message from The Moscow Times:
Dear readers,
We are facing unprecedented challenges. Russia's Prosecutor General's Office has designated The Moscow Times as an "undesirable" organization, criminalizing our work and putting our staff at risk of prosecution. This follows our earlier unjust labeling as a "foreign agent."
These actions are direct attempts to silence independent journalism in Russia. The authorities claim our work "discredits the decisions of the Russian leadership." We see things differently: we strive to provide accurate, unbiased reporting on Russia.
We, the journalists of The Moscow Times, refuse to be silenced. But to continue our work, we need your help.
Your support, no matter how small, makes a world of difference. If you can, please support us monthly starting from just $2. It's quick to set up, and every contribution makes a significant impact.
By supporting The Moscow Times, you're defending open, independent journalism in the face of repression. Thank you for standing with us.
Remind me later.