Just hours after Japan's Prime Minister Shinzo Abe sat down for his first substantial talks with China's Xi Jinping, three of his cabinet ministers Thursday visited the war shrine that Beijing sees as a symbol of Tokyo's violent past.

Visits by the three have the potential to muddy diplomatic waters that were starting to clear after their nationalist boss sat down with the Chinese president on the sidelines of a regional summit in Jakarta.

"I offered my sincere appreciation for the people who fought and sacrificed their precious lives for the sake of the country," National Public Safety Commission chief Eriko Yamatani told reporters after her pilgrimage.

"I pledged efforts for building a peaceful country," said the minister, known for her strident nationalistic views.

She was followed over the next few hours by Haruko Arimura, state minister in charge of female empowerment and internal affairs minister Sanae Takaichi.

More than 100 Japanese lawmakers went to the shrine on Wednesday to coincide with its spring festival, even as officials were making final arrangements for the Xi-Abe meet.

Abe had asked his ministers not to visit before the talks happened, according to Jiji Press.

Xi and Abe held discussions in Jakarta for about 30 minutes, their first lengthy pow-wow since both men came to the helm of nations that are bitterly at odds over history and current territorial disputes.

Abe later told reporters that they had a "very meaningful summit meeting" and bilateral relations were improving.

In Tokyo Thursday, Chief Cabinet Secretary Yoshihide Suga, speaking after Yamatani's pilgrimage, said it should have no bearing on warming China ties.

"I don't think there will be (any impact). The visit was made in a personal capacity."

- 'Unlikely to damage' -

Masaru Ikei, professor emeritus at Keio University and an expert on Japanese diplomatic history, said shrine visits like this were somewhat inevitable, but unlikely to be a disaster.

"It would have been better if cabinet ministers had stayed away, as well as the prime minister," he said.

But Abe could not stop ministers from going "in a private capacity", he said, pointing to the political need for conservative politicians to appease their support base.

"There is considerable repulsion among people (on the right) who believe Japan makes too many concessions" on history.

It is often said that Japan-China relations are cold politically but hot economically, he noted.

"There would be no point in worsening ties further when Abenomics seems to be bringing some benefits," he said, referring to Abe's pro-spending economic policies.

"I think it is unlikely to cause major damage" to ties, he added.

In a sign of how much history haunts relations in Asia, Abe's speech in Jakarta on Wednesday touched on World War II, but somewhat soft-pedalled, expressing "deep remorse" and not the "heartfelt apology" former prime ministers have proffered.

"I hope the Japanese side can take seriously the concerns of its Asian neighbours," CCTV News reported Xi as saying.

Yasukuni Shrine honours those who fought and died for Japan, but also includes a number of senior military and political figures convicted of the most serious war crimes.

Yamatani, Arimura and Takaichi are conservative female ministers who also visited the shrine during its autumn festival last year.

Abe, who has not visited since December 2013, sent a symbolic offering of a small tree on Tuesday, sparking anger from Beijing and Seoul.