Visiting Indonesian President Megawati Sukarnoputri voiced hope Monday that the ongoing dispute in Aceh Province can be resolved peacefully through dialogue.
She added, however, that her government will not tolerate any independence movement in the region.
Indonesian troops launched military attacks against Aceh separatists last month, immediately following the collapse of talks in Tokyo between Jakarta and the Free Aceh Movement (GAM) that were aimed at salvaging a peace deal.
"As Indonesia is recognized as a unified nation (under its constitution), we will not allow another form" of self-rule, Megawati, who is on a four-day state visit to Tokyo, told a news conference, at the Japan National Press Club.
She explained that while she supports a peaceful solution, an approach of this kind has certain limitations.
Megawati also voiced hope that the ongoing military operation in the resource-rich province of Aceh will be completed earlier than the six months initially predicted by the Indonesian Army.
The deal that was the focus of the Tokyo talks had helped quell an insurgency in the province that had lasted for more than a quarter of a century.
During a meeting with her Indonesian counterpart, Hassan Wirajuda, later Monday, Foreign Minister Yoriko Kawaguchi called on Indonesia to minimize civilian damage in the Aceh conflict and protect human rights.
Kawaguchi also stated that Japan is ready to support any new peace talks between the two sides, including providing a venue for negotiations.
Megawati is scheduled to meet Prime Minister Junichiro Koizumi on Tuesday evening, with discussions over a future bilateral free trade agreement high on the agenda.
She is the first Indonesian leader to make a state visit to Japan since 1968.
Prior to her news conference, she attended a welcoming ceremony at the State Guesthouse in Tokyo's Akasaka district with Emperor Akihito and Empress Michiko.