Yudhoyono said the pair had 'agreed on cooperation in dealing with avian influenza' during talks in the Indonesian capital.
'I have offered Prime Minister Abe bilateral cooperation in developing a human vaccine based on the Indonesian strain of the virus, for the sake of our welfare and the global interest,' he said.
Abe said Tokyo had decided to provide 1.7 billion yen (14.8 million dollars) in aid to help fight avian influenza.
Indonesia is the nation worst hit by the H5N1 virus and has reported 104 confirmed bird flu cases, with 83 deaths.
Jakarta has been rapped by the UN's World Health Organisation for failing to share its samples with the rest of the world, saying it will not formally hand more over until is guaranteed access to affordable medicines to treat victims.
Despite Indonesia's position however, a sample of the virus that killed a woman on Bali last week was sent to a WHO laboratory to allay fears that it has mutated into a form that can be transmitted between humans.
Scientists worry the bird flu virus could mutate into a form easily spread among humans, leading to a global pandemic with the potential to kill millions.