The fishing trawler captain, Zhan Qixiong, flew out of Japan on a chartered plane that took him to the coastal Chinese city of Fuzhou, but Beijing's response suggested it still harbored some rancor.
The release followed the detention of four Japanese nationals on suspicion of violating Chinese law regarding the protection of military facilities, though Japanese Chief Cabinet Secretary Yoshito Sengoku has denied a link between the two incidents.
China's Foreign Ministry said Beijing was angry at the detention of the captain, arrested by Japan over two weeks ago after his trawler collided with two Japanese patrol boats in waters near islands that both sides claim.
"This was an action that gravely violated Chinese sovereignty and the human rights of a Chinese citizen, and the Chinese government strongly protests," said a ministry statement issued after Zhan flew back to China.
China said its claim to the islands -- which it calls the Diaoyu and Japan calls the Senkaku -- was "indisputable."
"It is unlawful and invalid for Japan to detain and investigate the boat captain and to take any legal measures against him," said the statement said, which was issued on the Ministry's website (www.mfa.gov.cn).
"Japan must offer China an apology and compensation over this incident." It did not specify what compensation it wanted.
China's statement also said, however, that the two countries should solve their disputes through dialogue. Japanese Prime Minister Naoto Kan also said it was time for Asia's two biggest economies to put relations back on a steady footing.
"I believe it is necessary for Japan and China to handle matters calmly," he said in New York, where he attended the U.N. General Assembly.
The dispute has underscored the brittleness of ties long troubled by Chinese memories of Japanese wartime occupation and territorial disputes over parts of the East China Sea that could hold rich reserves of gas.
Some Japanese newspapers decried Zhan's release as a backdown that would encourage Chinese assertiveness.
"There is a possibility that it has left an impression that Japan will cave in when pressured," a leading daily, Asahi Shimbun, said in an editorial.
Sun Cheng, an expert on relations between the two countries at the China University of Political Science and Law in Beijing, said it would take time for relations to improve.
"China will want to keep up its case over the Diaoyu islands. Whether Japan actually apologies or gives compensation is not so much the point as making it clear that China won't compromise on sovereignty," he said.
A Japanese national resources and energy agency official said it was highly possible that China had started drilling in a gas field in another disputed part of the East China Sea, Kyodo news agency reported late on Friday. But the report also cited a Foreign Ministry official as saying there was no confirmation.
Before the captain's release, China canceled diplomatic meetings and student visits. Tokyo had said it feared a prolonged dispute could hurt ties between the world's second and third largest economies, now swapping places as China overtakes Japan to the No.2 spot.
Japan's sluggish economy has become increasingly reliant on China's dynamism for growth. China became Japan's biggest trading partner last year.
China also wanted to ensure that the lingering tensions did not badly damage trade ties, said Sun, the Chinese professor.
"It's not just Japan that needs China. China also needs Japan's markets, technology, investment," he said. "But this (dispute) will hurt relations for while yet."
(Additional reporting by Yoko Nishikawa and Chikako Mogi in Tokyo and Andrew Quinn in Washington; Editing by Nick Macfie)