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.
More than 600,000 Rohingya, who are not recognised by the Myanmar government as one of the country's many ethnic groups, have fled to Bangladesh since August a year ago, when violence between armed Rohingya and Myanmar security forces prompted a severe crackdown.
Japanese Foreign Minister Taro Kono asked Myanmar's leader Aung San Suu Kyi on Friday to ensure the "safe and voluntary repatriation and resettlement" of members of the Rohingya ethnic group who have fled to Bangladesh from Myanmar's strife-torn Rakhine state.
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's rare admission of wrongdoing comes after months of denying abuses in Myanmar's Rakhine state amid a military crackdown that has prompted about 655,000 Rohingya Muslims to flee to bordering Bangladesh and claimed at least 6,700 lives since August.
Prior to the joint news conference, the Japanese government announced emergency grant aid of around $3 million to Myanmar to help facilitate the return of the Rohingya.
It labeled the 400 dead as "extreme terrorists" who died during military "clearance operations".
In a district on the border with Bangladesh, Kono viewed the planned return route for hundreds of thousands of Rohingya refugees, including a small bridge close to the border under tight security control. Myanmar said it would start the process by January 23, but an actual figure on the extent of the repatriation is not yet known.
"It is a positive indication that we are taking the steps to be responsible", Suu Kyi said according to the report in the Global New Light of Myanmar newspaper.
India has also pledged to give Myanmar $25 million for development projects, including prefabricated houses in Rakhine state.