The Federal Security Service patrol ship Argal had chased the ship for eight hours, RIA Novosti reported.
The trawler, Sapsan, finally stopped when a security service patrol aircraft fired on it, the regional FSB branch said in a statement.
No one was hurt in the incident.
The 19 members of the trawler's crew were all Russian.
Officials speculated the vessel might have used for poaching. It was equipped to transport frozen and live crabs, but did not have the necessary technical documents or ship's log.
The Sapsan was escorted to the port of Petropavlovsk-Kamchatsky.
The captain faces administrative charges.