The two leaders, who spoke for about 15 minutes by telephone, also reaffirmed the need for their countries to cooperate closely to achieve progress in international talks taking place in Beijing on North Korea's nuclear program, Fukuda told reporters.
Fukuda did not say how the countries would cooperate.
Nine people, including a Japanese journalist, were killed Thursday when Myanmar security forces opened fire on groups of protesters in the main city, Yangon.
China is Myanmar's main economic and political ally, while Japan is its largest aid donor. Tokyo suspended grants for major projects after the junta violently suppressed pro-democracy protests in 1988, but has since given aid under a program focused mainly on health, education and humanitarian projects.
Fukuda said he also expressed his wish to visit China at an early date. Wen welcomed the comment and said preparations were under way for President Hu Jintao to visit Japan, according to a Japanese Foreign Ministry statement.
No timeframe was specified for Hu's visit. Media reports have said Fukuda is considering a trip to China later this year.
Separately, Fukuda also had a 10-minute telephone talk with South Korean President Roh Moo-hyun in which they agreed to work closely together to further develop bilateral ties, Roh's spokesman Cheon Ho-seon told reporters in Seoul.
The two leaders agreed to meet on the sidelines of a Southeast Asian summit meeting scheduled for November in Singapore, he said.
Fukuda, who took office earlier this week, is seen as a moderate compared to his nationalist predecessor, Shinzo Abe, who held unapologetic views regarding Japan's military actions in Asia before and during World War II.
Fukuda has vowed to pursue stronger relations with Asian nations such as China and South Korea, which still question Japan's dedication to peace more than 60 years after the end of the war.
The Chinese military believe that Beijing and Moscow must resist pressure from Washington together