TOKYO/BEIJING (Reuters) - Japan on Tuesday vowed to make a stern protest to China after a regional Chinese newspaper printed a map of the country with mushroom clouds hovering over the cities of Hiroshima and Nagasaki and accused the Japanese of wanting war again.

The neighbours have a long history of tense relations. Beijing bristles at Japan's inability to properly atone for its invasion of China before and during World War Two, and its occupation of large parts of the country.

The newspaper, the weekly Chongqing Youth News from the southwestern city of Chongqing, printed the picture in its latest edition, Chinese media reported, though it appeared later to have been removed from the paper's website version.

The picture showed a map of Japan with mushroom clouds over Hiroshima and Nagasaki - both of which were hit by nuclear bombs at the end of World War Two - and the words in Chinese and English, "Japan wants a war again".

A picture of the page was carried on the website of the Global Times, a widely-read tabloid published by the ruling Communist Party's official People's Daily.

"As the butcher of World War Two, the blood on Japan's hands has yet to dry," the Chongqing Youth News wrote in an accompanying article that remains available on its website.

Japanese Foreign Minister Fumio Kishida said the paper's comment and the accompanying map were regrettable.

"As foreign minister of the only country that has suffered nuclear attacks, and as a politician from Hiroshima, I cannot tolerate this," he told reporters.

"I issued an instruction to check the facts with the paper in question speedily through the consulate in Chongqing and, if it turns out to be true, to lodge a stern protest."

Calls to the newspaper seeking comment went unanswered. Its website says the newspaper is published by the Chongqing branch of the party's Youth League.

Japanese leaders have repeatedly apologised for suffering caused by the country's wartime actions, including a landmark 1995 apology by then prime minister Tomiichi Murayama. Japan's government, including Prime Minister Shinzo Abe, has repeatedly said that Japan has faced up to its past sincerely.

But contradictory remarks from conservative politicians have cast doubt on that sincerity.

(Reporting by Kiyoshi Takanaka and Ben Blanchard; Editing by Clarence Fernandez)