The four-day camp, which ended on Thursday, included religious lectures, visiting local mosques and aerobics workouts.
"They have crossed the line...we are disgusted and offended that a child's feminine traits or behaviour is seen as being something that is evil and that should be purged," said Ivy Josiah, a child's rights campaigner and executive director of the Malaysian rights group, Women's Aid Organisation.
The schoolboys, aged 13 to 17 and living in the northeastern Malaysian state of Terengganu, were selected for the boot camp for displaying "some feminine characteristics", state education department director Razali Daud was quoted as saying in the New Straits Times newspaper on Tuesday.
The camp's establishment was prompted by what Razali said was a rising number of effeminate schoolboys in the state.
Homosexuality is a taboo subject that is rarely discussed in this mainly Muslim country and sex between males is an offence punishable under criminal law.
Razali subsequently told the newspaper on Thursday that the camp was a character-building programme and was not aimed at changing the students' sexual preference. He declined to comment when contacted by Reuters.
Senior state and federal education officials also refused to comment after the issue prompted widespread criticism. "Corrective boot camps to 'fix' children and individuals must not be condoned because it violates the rights of people who are perceived as 'different'," a coalition of gender equality groups said a statement.
The country's Women, Family and Community Development Minister Shahrizat Abdul Jalil has called for such camps, of which this was the first known example in Malaysia, to be abolished.
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