Human rights groups on Friday demanded Indonesia to revoke a law which they claim to have effectively legalised female circumcision.
Women's rights activists called on the government to withdraw a decree issued by the health ministry in November authorising certain medical professionals to carry out the procedure on baby girls.
"We are very disappointed with the minister's decision. Circumcision is a form of abuse of women," said Aditiana Dewi Eridani of the Islam and Women's Rights Information Centre.
"This is a backward step for women's rights protection in this country."
The practice is encouraged by some Islamic leaders and is common in the mainly Muslim country, especially in more conservative rural communities.
Amnesty said the decree violated several Indonesian laws on human rights, child protection and discrimination against women.
"Female genital mutilation constitutes a form of violence against women which should be eradicated," it said in a statement.
It said the practice "inflicts pain and suffering on women and girls, and hence violates the absolute prohibition of torture and ill-treatment".
"Female genital mutilation also encourages discriminatory stereotypes about women?s sexuality," Amnesty added.
Health ministry director of mothers? health, Ina Hernawati, told the Jakarta Globe newspaper the decree did not legitimise female circumcision.
"We do not condone the practice. If parents come to midwives, we ask the midwives to explain that medically female circumcision is useless," she was quoted as saying.
But she said many parents wanted their baby girls circumcised for religious reasons and in such cases it was better if it was done by a "trained health worker rather than some random shaman".
She also rejected the idea that female circumcision was a form of genital mutilation.
"Circumcising is merely scratching a piece of skin," she said.
Amnesty said Indonesian parents typically wanted their girls circumcised for religious or health reasons, or to suppress their daughters' sexuality in adulthood.