Indonesia has been urged to stop virginity tests for female military applicants, with human rights activists calling the practice "cruel, inhuman and degrading".

Human Rights Watch (HRW) said the examinations, normally carried out through a test to ensure the hymen is intact, are a form of gender-based violence and "scientifically baseless".

The Indonesian military defended the practice, saying that people of low morals could "damage the military".

"If a person has low morals, then she cannot join the military. Because if she joins the military it will damage the military, which must handle a huge duty," military spokesman Fuad Basya said.

"They are responsible for the country's sovereignty, the unity of the territory, the safety of the nation."

Indonesia denies it also checks women who are planning to marry officers.

This is just the latest controversy around virginity tests in Muslim-majority Indonesia, with the police facing criticism last year for subjecting female applicants to undergo the examinations.

The HRW said the military "should immediately end the use of so-called virginity tests, which violate the prohibition of cruel, inhuman, and degrading treatment under international human rights law".

The group interviewed 11 recruits and officers' fiancees who had undergone the tests at military hospitals on the main island of Java. They also spoke to people involved in conducting the tests.

Those examined described the practice as painful, embarrassing and traumatic.

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"I felt humiliated. It was very tense," said one applicant tested in 2013, cited anonymously in HRW's report.

She added that she was "shocked" that the doctor performing the test was a man.

"It's against the rights of every woman," she said.

The test has been standard for decades and one retired air force officer, also cited anonymously, recalled having it done in 1984.

She said four years later she got married but could not make love to her husband for months "because of the trauma that I had with that 'virginity test'."

The HRW report comes ahead of a meeting next week on the island of Bali organised by the International Committee of Military Medicine, a body that fosters cooperation between medical services of armed forces worldwide.

AFP