
Japan, however, did not say whether would end all assistance to the country.
Japan's Foreign Minister Masahiko Komura said Japan was cancelling grants of up to 552 million yen (US$4.7 million, around 18 percent of the total grants and technical assistance Tokyo gave Burma last year.
"The Japanese government needs to show our stance. We cannot take action that would effectively support the military regime at this moment," Komura told reporters.
Japan, in a rare break with the United States and the European Union, has been one of the largest donors to Burma.
The cancelled grants had been intended to finance the construction of a human resources centre in Burma. It was the only concrete grant aid project for which Japan was exchanging notes with the government.
"We presume there will be some requests in the future. We will make a judgement on each case by looking at the situation at that point of time," said a government official who declined to be named.
Among the victims of the Burma's crackdown on peaceful protesters was Kenji Nagai, a video journalist for Tokyo-based APF News, who was killed on September 27 as he filmed the crackdown in Rangoon.
Television footage showed him apparently being shot at close range by security forces.
The state-run New Light of Myanmar on Monday said Nagai's death was an accident but complained that Nagai "dishonestly" entered the country on a tourist visa.
"He met his tragic end due to the fact that he was together with the protesters at an improper site at an improper time," it said, adding that Burma had a "magnanimous" attitude towards Japan.