The controversy centres on the opening of the new Atomic Bomb Museum, a 41-year-old landmark which commemorates in gruelling detail the prologue and aftermath of the city's destruction on 9 August 1945, six days before Japan's surrender.
For years, critics inside and outside Japan complained that while the museum made much of the suffering of the bomb's victims, it failed to explain the events leading up to its use, especially Japanese atrocities in Asia during and after the Second World War. The revised exhibit was intended to remedy this. But after anonymous phone threats and complaints by conservative members of the city assembly, the museum's administrators have removed several of the exhibition's most controversial elements.
Photographs of Chinese civilians massacred by the Imperial Army during the notorious Rape of Nanking in 1937 have been replaced with those of victorious Japanese soldiers marching into the city.
Pictures of the so-called Bataan Death March in the Philippines, during which thousands of Allied prisoners of war died of hunger, torture or exhaustion, have been removed; in their place will be photographs of Japan's lightning attack on Pearl Harbor.
According to the Nagasaki Shimbun newspaper, printed texts in Japanese and English have been altered to delete such passages as the following: "Harbouring feelings of inferiority towards the West on the one hand, and of superiority towards Asia on the other, Japan began to walk down the road towards colonial domination of China and Korea."
Panels focusing on foreign prisoners killed by the atom bomb, and Japanese aggression before and during the war, have been replaced by photographs of the bloody battle of Okinawa, in which 147,000 Japanese civilians died under an American bombardment.
Yoichi Tanaka, the director of the city's atomic bomb survivors' department, insists that the changes were made voluntarily in order "to describe history more objectively."
Privately, however, the city officials are in no doubt that the museum has bowed to right-wing elements who still maintain the justice of Japan's war and who resent any suggestion that the country brought the atomic bombings on itself.
Earlier this month, 11 local dignitaries, including the chairmen of the Nagasaki Chamber of Commerce and the chief priest of the city's biggest Shinto shrine, sent a letter of complaint on behalf of an organisation calling itself the "Society of the Rising Sun".
"There are a number of conflicting arguments about the actuality of events such as the `Rape of Nanking', `comfort women' and `forced labour'," it read.
"Presenting an exhibition... when there is absolutely no consensus about these events will hinder the objective and accurate understanding of visitors". Apart from a dozen letters making similar complaints, the museum has also received threatening phone calls.
Finally last month, a group of conservative members of the city assembly lodged a formal protest.
City officials expect noisy demonstrations when the exhibition formally reopens on Monday. The spectacle of black vans draped with rising-sun flags and blaring martial music is familiar in Japanese cities, but in Nagasaki it has a particularly sinister resonance. In 1990 a former mayor of the city, Hitoshi Motoshima, was shot in the back and critically injured by a right-winger after he stated that the late Emperor Hirohito "bore responsibility for the war".
In the run-up to the 50th anniversary commemorations last August, controversies about the war smouldered on both sides of the Pacific. The former prime minister Tomiichi Murayama laboured for months to pass a resolution in the Diet apologising for the country's wartime misdeeds. But even a watered- down compromise motion was angrily denounced by the right.
Ironically, the Smithsonian Institution in Washington ran into similar trouble last year for diametrically opposite reasons to those dogging the Nagasaki museum. An exhibition about the Enola Gay, the B-29 plane which bombed Hiroshima three days before the attack on Nagasaki, was criticised for focusing on the consequences of the attack, and for raising awkward questions about the necessity of the bombing.Reuse content