The Myanmar military has admitted that the members of its security forces were involved in the killing of 10 Rohingya Muslims whose bodies were found in a mass grave in December in restive Rakhine State.
Suu Kyi was speaking following a meeting in Myanmar's capital Naypyidaw at which Kono asked her to ensure the "safe and voluntary" resettlement of those who have fled, according to Japanese news agency Kyodo.
As of December 2017, an estimated 6,55,000 Rohingya people fled to Bangladesh to avoid the persecution from the security forces that started in Myanmar's Rakhine state in August previous year.
Aung San Suu Kyi stressed the importance of the rule of law and said the military would take responsibility.
In response to Myanmar's military's admission of killing Rohingyas, Amnesty International said on Thursday that the confession is just the "tip of the iceberg".
Rohingyas who fled from the persecution of Myanmar security forces want to see a positive development including citizenship, security, and scope for enjoying their basic rights before they return to their country from Bangladesh, the UNHCR said recently.
The government of Buddhist-majority Myanmar does not acknowledge Royingya as a minority group even though they have lived in the country for generations.
The UN and United States have accused Myanmar's army of ethnic cleansing, with the UN rights chief saying it may even be guilty of genocide.
More than 655,000 Rohingyas have crossed into Bangladesh since August 25 past year, escaping a military crackdown in the Rakhine state, which many countries and human rights bodies have described as ethnic cleansing.
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.