Addressing the sailors on the returning ship, Shigeru Ishiba, Japan's defence minister, thanked them for completing their duties.
"Many countries are calling on us to renew our efforts in the war on terrorism. I will do all I can to see that our refueling mission can begin again as soon as possible,'' he said.
On Thursday Fukuda made a renewed pitch for an extension to the mission after he promised George Bush, the US president, during a recent visit to Washington that he would try to restart the deployment.
The six-year mission was brought to an abrupt end on November 1 after Japan's opposition parties raised concerns that it was too broad and possibly violated the country's pacifist constitution.
Japanese destroyer Kirisame, the other ship in the mission, returned to a southern port on Thursday after four months at sea.
Fukuda's government is pushing for Japan to develop a higher profile in international diplomacy by increasing its involvement in global peacekeeping missions.
The leadership is also trying to secure a permanent seat on the United Nations Security Council.
But the opposition, after winning control of the upper house of parliament in July, vowed that Japan should not take part in what it calls "American wars".
Last week, the government-controlled lower house of parliament approved a watered-down mission in the Indian Ocean, and the law is now in the opposition-controlled upper house.
The proposed revised mission was to be limited to supplying fuel and water in operations related to monitoring and inspecting vessels suspected of links to terrorism or arms smuggling.
Japanese ships would not be refuelling coalition vessels directly involved in combat activities in Afghanistan.
The defence ministry said Japan had provided about 490,000 kiloliters of fuel to coalition warships in the Indian Ocean since 1991.