"At this very moment in the Indian Ocean, numerous countries are cooperating, carrying on their fight against terrorism," he said.
"I want Japan to be working hard for the world along with other countries as soon as possible.''
For six years Japan's naval mission provided logistical support to forces involved in the war in Afghanistan, primarily supplying fuel to coalition warships.
But the mission was recalled on November 1 after Japanese opposition parties raised concerns that the operation did not have explicit support from the United Nations.
Critics also suggested that the mission possibly violated Japan's pacifist constitution.
Embarrassing retreat
Japan has conducted refuelling missions since
The retreat was a major embarrassment for Fukuda, who has been a staunch supporter of a continued presence for Japan in the region, and threw a cloud over Japan's close alliance with the US.
Fukuda's government has now submitted a bill to parliament to allow the ships to be deployed again, but in a more limited role.
His ruling bloc is expected to use its majority in the powerful lower house to push the bill through the upper chamber, which is controlled by the opposition.
Under the new bill, the Japanese mission would be limited to refuelling and supplying water to ships used in monitoring and inspecting vessels suspected of links to terrorism or arms smuggling.
The Japanese ships would not though refuel coalition vessels directly involved in military operations inside Afghanistan.
In his New Year's message, Fukuda also promised to spearhead efforts to tackle global warming in 2008 after Japan takes over the presidency of the G8 group of industrial countries from Germany.
Japan has fallen far behind its Kyoto Protocol commitment to cut greenhouse gas emissions.
"By sharing the world's most advanced technology, Japan is prepared to play a major role"' in the fight against climate change, Fukuda said.