Foreign Minister Fumio Kishida said Japan remained committed to helping national reconciliation efforts on various fronts in Asia, including between Myanmar's government and "ethnic minority groups".
"With regard to non-regular immigrants, including women and children trying to cross the Indian Ocean, Japan has decided to extend $3.5 million" through global agencies such as the UN High Commissioner for Refugees, he said in a public address.
The money will go to providing food and shelter as well as to fund data analysis of their maritime movements, the foreign ministry was quoted by AFP as saying.
The plight of the persecuted and impoverished Rohingya has drawn international attention as thousands of them and Bangladeshi migrants cram into boats and struggle desperately to reach other Southeast Asian countries.
The Muslim Rohingya complain of systematic discrimination and mistreatment by Myanmar's Buddhist-majority government, which refuses to even recognize them as citizens.