As of Thursday, 595 refugees had returned, including 452 from Mahama camp and 143 from other cities. The other 1,503 returned to their country in three batches.
The ministry said it would continue to help the rest return to their homeland in peace.
The majority of the refugees fled the country following the political crisis that gripped Burundi in 2015 when the then President, the late Pierre Nkurunziza decided to seek a third term, leading to countrywide protests as people opposed the move.
The first batch of refugees returned on August 27 and was welcomed by the President of Burundi, Gen Maj Evaritse Ndayishimiye.