The German firm was one of only four maritime companies known to have suspended shipments to Tokyo Bay due to radiation concerns from Japan's Fukushima nuclear plant, located 240 km (150 miles) north of the capital.
"Our vessels will be calling again at the ports of Tokyo and Yokohama as of week 14," Hapag-Lloyd said on its website in a news release dated March 30.
"This decision was made after radiation measurements in the Tokyo Bay area showed stable and decreasing values for a number of days."
The vast majority of the shipping industry have maintained their operations at the two ports following daily assurances from the Japan's transport ministry that radiation in Tokyo Bay was at a very safe level.
Yokohama is Japan's largest port, handling 271 million deadweight tonnes of cargo in 2010, while Tokyo was No. 4 with 156 million, according to Lloyd's List Intelligence.
Hong Kong's Orient Overseas Container Line and Germany's Hamburg Sued have also resumed calling at the ports after a brief disruption.
German container ship operator Claus-Peter Offen is believed to be the only maritime company still avoiding the Tokyo Bay area due to radiation fears, shipping officials said.
Officials at Claus-Peter Offen were not immediately available for comment.
Although radiation fears have eased for the shipping industry in Tokyo, the situation at the Fukushima nuclear plant has improved little three weeks after the March 11 disaster. Seaborne traffic has been restricted near the facility.
Japan's government on Monday told the operator of the plant to move quickly to stop radiation seeping into the ocean as desperate engineers resorted to bath salts to help trace a leak from one reactor.
One official has warned it could take months before the nuclear crisis is under control. (Reuters)
