The Indonesian government announced in December that it would fingerprint all students at Islamic boarding schools, or pesantren.
It said the move was part of its national anti-terror drive, which has been given fresh impetus by the second Bali bombings and the renewed violence in central Sulawesi, where three Christian schoolgirls were recently beheaded.
Following an immediate outcry over the announcement, the government decided that all Indonesians would be fingerprinted.
The pesantren issue has been gathering pace for some time and has been exacerbated by several recent events.
The sentencing of Abu Bakar Basyir - a principal of an Islamic school in East Java and the alleged head of the suspected JI terror network - for his role in masterminding the bombings in Jakarta and Bali have given the pesantren question an added edge.
The expulsion by the state of a number of Indonesian students from pesantren that were believed to have links with militants in Pakistan has further added to the controversy.
Another factor has been the role played by a school principal in West Java in an attack on the property of Ahmadiyah, a dissident Muslim sect.
The pesantren schools have been strongly criticised for offering an attenuated curriculum that consists of reciting the Koran, performing menial tasks around the compound and some physical drill.
The government's initial announcement was questioned by a number of figures, including Sidney Jones of the International Crisis Group's Indonesia bureau.
Ms Jones, who was herself recently excluded from the country on apparently arbitrary grounds, said that half of those already sentenced in Indonesia for terror activities, including the first Bali bombing, had attended state schools.
Leading Muslim figures also said the proposed fingerprinting plans were discriminatory.
Despite having the world's largest Muslim population, Indonesia is not an Islamic state and officially promotes religious tolerance.
Inter-communal religious violence, especially in the Moluccas and Sulawesi, has placed this tolerance under severe strain. The government is now concerned not to allow schools to become platforms for the promotion of religious extremism.
Christian schools, for example, are allowed to accept Muslim students.
However, official monitoring of religious schools - including pesantren - appears to be lax.