The four men used samurai swords to attack officers at Riau police headquarters in Pekanbaru, Sumatra, national police spokesman Setyo Wasisto said.
In addition to the two injured cops, one police officer killed after getting hit by suspected terrorists' vehicle, one journalist injured, four perpetrators killed while at least one is on the run.
Local media said one attacker may have had a bomb strapped to his body but police have not confirmed the reports.
Its worst-ever attack was the 2002 Bali bombings that killed more than 200 people, including locals and foreign tourists.
Editor's note: An earlier version of this article stated that at least three men had attacked the Riau Police headquarters.
The attack followed multiple terrorist strikes recently in the country, including the riot in a jail in the capital last week, suicide bombings in three churches on Sunday in Surabaya city, the provincial capital of East Java, and a suicide bombing in the police headquarters in the city, which left at least 28 dead with dozens injured.
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Indonesia's security forces have arrested hundreds of militants during a sustained crackdown that smashed some networks, and most recent attacks have been low-level and targeted domestic security forces.
All six bombers were killed, including the mother who was Indonesia's first known female suicide bomber.
The church bombing family were in the same religious study group as the Surabaya police station bombers and a third family believed to be linked to the wave of attacks, authorities said.
On Monday members of another family blew themselves up at a police station in Surabaya, wounding 10.
The Islamic State (IS) group has claimed the attack via its news outlet.
The police shot two of them, Doddy said.