Rights groups have accused Nobel Laureate Suu Kyi of failing to condemn the widespread abuses during the army crackdown, which followed raids by militants from the Arakan Rohingya Salvation Army (ARSA).
"Japan wants to actively support Myanmar's efforts", including in Rakhine, he said at a joint press conference after their meeting in Nay Pyi Taw.
It noted that Taro Kono planned to meet with Aung San Suu Kyi and military leader Min Aung Hlaing as well as visit Maungdaw Township in northern Rakhine State.
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Aung San Suu Kyi stressed the importance of the rule of law and said the military would take responsibility.
On Wednesday the military acknowledged that security forces and villagers were responsible for the deaths of 10 people found in a mass grave in December.
"We have chose to provide the aid in response to the agreement between Myanmar and Bangladesh to represent an worldwide message of support so that the repatriation can be carried out promptly", said Foreign Ministry official Shinobu Yamaguchi in a statement. It said the 10 were "terrorists" who threatened villagers.
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The European Union (EU) urged Myanmar to allow the United Nations (UN) to access the country for conducting the probe into the Rohingya assaults reported so far.
The army, which is not under the control of the civilian government, launched a sweeping counteroffensive in northern Rakhine in response to Rohingya militant attacks on August 25, triggering an exodus of more than 650,000 Rohingya villagers to Bangladesh.
Rohingyas are a Muslim minority ethnic group in Myanmar.
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Myanmar does not consider the Rohingyas to be citizens, treating them mostly as Bangladeshi immigrants and imposing many restrictions on them, including on their freedom of movement within the country.