A sealed wagon attached to a passenger train transported the group from the northern city of Murmansk to St. Petersburg's Ladozhsky Station, the officials said.
While Russia has not given an official reason for the transfer, it comes after widespread international protests over the arrest of the 28 crew members, Russian photographer and a British videographer aboard the Greenpeace ship.
The two Canadians are Paul Ruzycki of Port Colborne, Ont., and Alexandre Paul of Montreal.
St. Petersburg is a more accessible destination for the activists' lawyers and family members than Murmansk, a far-flung city north of the Arctic Circle that gets little light during its long winter.
State television said the activists were taken to three detention centres, including the notorious Kresty prison. Built in 1893, Kresty is the oldest detention centre in St. Petersburg and many political prisoners have been among its inmates.
Greenpeace International Arctic campaigner Ben Ayliffe said in a statement that the organization did not know which pre-detention centre the activists would be taken to in St. Petersburg.
In late October, Russia dropped piracy charges, which carry a sentence of up to 15 years. The 30 are now charged with hooliganism, which carries a maximum sentence of seven years.
The ship, the "Arctic Sunrise," was seized by the Russian coast guard on Sept. 18 and all crew members were arrested after staging a protest outside of an oil rig owned by Russia's Gazprom state energy giant.