Yasukuni Shrine honours Japan’s war dead, including some senior military and political figures convicted of serious crimes in the wake of the country’s Second World War defeat.

That, and the accompanying museum - which paints Japan as a frustrated liberator of Asia and victim of the Second World War - makes it controversial, especially in China and South Korea, where it is seen as a symbol of Japan’s lack of penitence.

Abe and other nationalists say the shrine is merely a place to remember fallen soldiers. They compare it with Arlington National Cemetery in the United States.

Masaru Ikei, an expert on Japanese diplomacy and professor emeritus at Keio University, said with Obama due to arrive on Wednesday for a state visit, Abe was always likely to stay away.

“The prime minister does not want to worsen ties with China and South Korea before President Obama’s visit, but he does want to maintain his creed that he should pray for the war dead,” he said.

Ikei said Washington’s very public and slightly unexpected rebuke after his last visit meant Abe “will not be able to visit the shrine again for a while”.

Japan’s chief government spokesman Yoshihide Suga on Monday sought to play down Abe’s shrine gift.

“I’m aware that the prime minister offered Masakaki (sacred tree),” he told reporters.

“The offering was made in his capacity as a private person, and so the government should not comment on such an act by him.”

Asked about possible ramifications on the upcoming meeting between Abe and Obama, Suga said: “It won’t affect the summit at all.”

Many conservative lawmakers are expected to go to the shrine to mark the spring festival on Tuesday.

Two of Abe’s cabinet ministers have already visited, saying they did not want the visits to interrupt their official duties.

Yoshitaka Shindo, Japanese minister for internal affairs and communications, provoked outrage when he visited the shrine two weeks ago. He said it was a "private matter" and Japan's foreign ministry said Shindo's grandfather had fought in the war.

Some countries see the Yasukuni shrine, which honours Japan's war dead including 14 war criminals, as a symbol of Japan’s refusal to come to terms with its wartime past, and have criticised Japan for "provoking its neighbours" when officials including Abe have paid visits to the shrine.

Ties with South Korea have shown slight signs of improvement recently, following a three-way summit between Abe, Obama and President Park Geun-hye and the visit to Seoul last week of a senior Japanese diplomat.

But relations with China remain sour.

In a further sign of their parlous state, Japanese shipping giant Mitsui O.S.K. Lines said China had seized one of its ships in a row over what Beijing says are unpaid damages relating to events in the 1930s.

That came after Japan began building a military installation in the far southwest of its long island chain, near the disputed Senkaku Islands, which Beijing claims as the Diaoyus.

The facility will bolster its ability to surveil China and is likely to further irritate Beijing, which regularly warns that Japan is re-militarising, while ramping up its own military spending and capacity.