Prime Minister Yoshihiko Noda called the incident "extremely regrettable." Other ministers said they will study how they can block future landing attempts, including possibly increasing the penalty for illegally landing on the island.
"Illegal entry and landing with the specific purpose of violating our country's territorial sovereignty should carry heavier punishment than usual," National Public Safety Commission chief Jin Matsubara said.
The arrests have prompted protests in Hong Kong and Beijing, and Japan's move to quickly deport the activists was seen as an attempt to avoid further inflaming protests.
Seven of the 14 activists left on a commercial flight from Japan's southern island of Okinawa, and the others were being flown to a nearby island to take their boat home later Friday from there, Justice Ministry officials said.
China had demanded immediate release of the activists, saying their capture by Tokyo was hurting bilateral relations.