Twenty-four others have been taken in for questioning.
The attacks were carried out this week. They raised concerns about escalating religious intolerance in Indonesia - a secular but predominantly Muslim nation.
Police spokesman Col. Boy Rafli Amar said Friday that two people have been arrested for the killing of Ahmadiyah Muslim sect members in Banten province.
Eight suspects were arrested in the Central Java town of Tamanggung, where a mob stormed a courthouse and set two churches on fire because of what they called a "lenient" prison sentence given to a Christian convicted of blaspheming Islam.