The last available figures on religion were collected in 1992 (before independence), at which time about the population was 90% Roman Catholic, 4% Muslim, 3% Protestant, 0.5% Hindu and an undetermined number were Buddhist. As of 2002, the dominant religion still appeared to be Catholicism; however, it is believed that a number of registered Catholics actually practice traditional animism, a religious category which had not been officially recognized by the Indonesian government.
The new government has generally respected the regulations for freedom of religion that were established by the UNTAET administration. Though public opinion had leaned toward making Catholicism the national religion, the presiding Bishop Carlos Filipe Ximenes Belo (a Nobel Peace Prize laureate) encouraged members of the Constituent Assembly not to make such a designation. The 2002 constitution instead provides for the separation of church and state.
Due to past associations with Indonesian occupation groups, some Muslim and Protestant minorities have reported social harassment.