President Susilo Bambang Yudhoyono, who has been criticised for failing to quell the violence, ordered the police and military to go "all-out" against extremists behind the unrest.
"Every person should be guaranteed protection and safety, whatever his faith, ethnicity, race, political affiliation or profession," he said in a speech to provincial governors.
Until recent months, Indonesia had been admired as setting an example of inter-faith harmony but by violent Islamic extremism and vigilante groups have eroded this image.
Sunday’s murder of three followers of the minority Ahmadiyah Islamist sect by a group of Muslims marked the climax of the wave of hate crimes targeting Christians and other minorities.
On Tuesday another crowd of Muslims set fire to two churches and vandalised a catholic school in Temanggung, Central Java.
The violence has drawn widespread international concern. Italian Foreign Minister Franco Frattini described Tuesday’s scene as a "very serious demonstration of anti-Christian fanaticism".
US Ambassador Scot Marciel said the US "joins the vast majority of Indonesians in deploring the violence" against the Ahmadiyah sect, and noted "with concern" the church burnings in Central Java.
Central Java provincial police spokesman Djihartono said almost 1,200 extra security personnel including troops had been deployed in Temanggung in response to Tuesday's unrest.