Local medai reported that dozens of protestors and police were injured before calm was restored on Wednesday.
Church-goers became angry when a Protestant man committed unspecified disrespectful acts during a mass at the Immaculata Cathedral Catholic Church in Atambua district town of Belu.
Police apprehended the man and took him for questioning, but according to a report on the Detik.com online news service, the Christians demanded the suspect be released to face mob justice.
When police refused, angry Christians went on a rampage, said Adjunct Senior Commissioner Ekotrio Budidarma, chief of Atambua's district police.
Several clashes took place, leaving dozens of protestors and police officers injured, Budidarma said. Calm was restored by Wednesday evening, he said.
Quelling a riot
Catholic priest Anton Pain Ratu, appealed for an end to the vandalism.
Local police, backed by army troops, were deployed to guard strategic points in the area to prevent further rioting.
The region has been the scene of many clashes between Christians and Muslims. Local authorities often keep the details of clashes secret to avoid further inflaming communal tensions.
Christians make up an estimated 10% of Indonesia's 210 Muslim majority population.