Germany's top diplomat, who is also deputy chancellor, met Japan's Prime Minister Yukio Hatoyama and Foreign Minister Katsuya Okada at the start of an Asia tour that will also take him to China.
"Disarmament is the central issue of our times," Westerwelle told reporters. "Germany wants it. Japan wants it too. The question now is what we can achieve together on the international stage."
He said Tokyo and Berlin must take a united stance to prevent the possibility of a nuclear-armed Iran.
Okada later told a joint press briefing: "If Iran holds nuclear weapons, that would be a very grave issue as we would not be able to stop the trend of nuclear proliferation in the world."
The Japanese foreign minister added that if talks with Iran failed and "if the international community decides to put sanctions on Iran, Japan would not
hesitate in joining the sanctions."
Hatoyama, in his talks with Westerwelle, "stressed the importance of cooperation between Japan and Germany as non-nuclear-armed nations in G8 that share the same value," said a Japanese foreign ministry statement.
On climate change, Hatoyama said the Copenhagen Accord reached last year was not satisfactory, while Westerwelle also spoke of the need for a binding international agreement, the statement said.
On Afghanistan, Okada told the press conference: "We agreed that there are areas where Japan and Germany can cooperate in helping Afghanistan."
Both sides agreed to cooperate in building a hospital in northern Afghanistan and discussed the need to boost police training and payments and to build up key sectors of the country's infrastructure.
"Schools, roads, water, energy - all this must be developed in order to bring self-sustaining security to Afghanistan," said Westerwelle.
The German foreign minister said both sides also discussed stepping up their long-standing bids for permanent seats on the UN Security Council, saying that "the forum should better reflect the world of the 21st century."
The ministerial meetings were the first since new governments took power in Tokyo and Berlin.