"They have fled unimaginable persecution and taken shelter to our country," he told reporters after a programme in Dhaka on Wednesday.
The minister said he recently visited Cox's Bazar, the southeastern district where the Rohingya refugees have taken shelter and spoke to many of them.
"Of the women, 90 percent were raped while all the children were wounded," he said.
The Myanmar Army launched the operation after Rohingya insurgents attacked security forces on Aug 25.
At least 380,000 Rohingyas have fled the violence into Bangladesh since that day, according to the UN.
Bangladesh, earlier, sheltered another 400,000 Rohingyas who fled persecution in Myanmar over the decades.
He, however, admitted that Bangladesh's social system could be 'disturbed' by the influx of Rohingyas.
He said the authorities were taking steps to stop the refugees from spreading.
He noted that the refugees would be provided with biometric identity cards.