Japan says Malaysian opposition leader Anwar Ibrahim was barred entry to Japan at the weekend because he did not obtain a visa.
Mr Anwar had arrived at Narita International Airport on a personal visit early Sunday but was turned away by immigration officials, who cited his controversial 1999 conviction for sodomy and corruption.
Mr Anwar speculated that "hidden hands" were behind the refusal, and his party questioned whether Malaysia's ruling coalition played a role.
However, embassy official Tomoko Nagai says that while Japan lifted a requirement that Malaysians obtain visas to enter the country last year, Mr Anwar is still required to have one due to his past criminal record.
She says Mr Anwar did not apply for a visa, as he had for previous visits.
"Japan could not consider a special arrangement for Anwar since we did not receive any prior application for a visa," she said.
Mr Anwar had been invited by a Japanese NGO to deliver a speech on religious harmony.
He was once heir-apparent to the leadership of Malaysia's ruling coalition but was cast from power over the sodomy and corruption charges - viewed by many as a set-up by his political enemies.
He was jailed in 1999 for six years.
After being refused entry, Mr Anwar said he was "puzzled and shocked" and demanded explanations from the Japanese and Malaysian governments.
Foreign Minister Anifah Aman dismissed any involvement by the Malaysian government.
Beginning with the 2008 elections, the ruling coalition has steadily lost ground in parliament to an Anwar-led opposition.
The opposition accuses the coalition of a long-running campaign of harassment including trumped-up criminal charges designed to smear Mr Anwar and trip up the opposition's surge.