It reported that hundreds of thousands of them fled violence in western Myanmar.
The call from the European Union came a day after the Myanmar army acknowledged it carried out extrajudicial killings of Rohingyas in the state.
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 a year ago.
"These brutal killings confirm the urgent need for a thorough and credible investigation into all violent incidents in northern Rakhine State to ensure the accountability of those found responsible for committing atrocities", it added.
During a meeting on Friday, Kono asked Suu Kyi's government to allow humanitarian and media access to the affected area, the resettlement of returned refugees, and the implementation of recommendations made by former United Nations secretary-general Kofi Annan.
"Japan is willing to help [the Myanmar government] make the country a place where communities from different faiths can live together peacefully", Kono said to the village chief.
On August 25, the Myanmar Army had launched a military offensive after Rohingya rebels had mounted a series of attacks on multiple government posts.
Around 650,000 Rohingyas subsequently crossed the border and sought refuge in Bangladesh.
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 past year, when violence between armed Rohingya and Myanmar security forces prompted a severe crackdown. 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.
Many refugees start at transit centres set up along the Bangladesh-Myanmar border before they are brought to the main refugee camps in Cox's Bazar.