The UN sent Pinheiro to investigate allegations of widespread abuse during the violent crackdown on pro-democracy protests in September which the government said killed 10 people.
Diplomats and dissidents say the toll is probably much higher and Amnesty International has estimated that 700 people arrested are still in detention.
The government continued to crack down on suspected protesters even during Pinheiro's stay.
In the latest sweep, the government detained at least three people who were handing out anti-government pamphlets on Wednesday at a marketplace in Yangon.
"Until the generals' military hardware is crumbled, they won't listen to anyone"
Oomlwin, Yangon, Myanmar
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The leaflet included a statement from the UN and one saying that forcing people to participate in pro-government rallies violated international human rights conventions.
Major-General Aye Myint, the deputy defence minister, said there had been some arrests, but suspects were only taken in for questioning.
He said 49 people were being detained in Yangon and 42 in other cities, without specifying when the arrests were made.
"After questioning, most of them are released," he said. "We will be taking actions according to the violation of the law and also the terrorism act.
"Now the situation in Myanmar is in normalcy. We totally control all the situation," Aye Myint told a news conference in Singapore after attending a meeting of South-East Asian defence chiefs.
He added that the generals would "not accept" outside interference they deemed harmful to their country's sovereignty.
"But we are also looking forward to the positive and constructive assistance and understanding from Asean countries, and all other countries from the world, and also the United Nations," he said.
The defence ministers' gathering was held ahead of the annual Association of South-East Asian Nations summit next week to be hosted by current chair, Singapore, and Myanmar is expected to be a dominant topic at the meeting.
Ong Keng Yeong, Asean's secretary-general, rejected calls by human rights groups to prevent Myanmar from signing a landmark Asean charter, which will for the first time call for the establishment of a human rights body in the bloc.