While the police managed to shoot four of the attackers, the remaining five escaped said the police chief of Riau.
Two policemen were injured in the sword attacks and another was killed after being hit by the minivan which was trying to escape the compound of the headquarters, he added.
The attacks have put Indonesia on edge as the world's biggest Muslim majority country starts the holy fasting month of Ramadan from Thursday.
Separately, Sunarto said police are still searching for more attackers.
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He said: 'But I don't want to say that I am happy with these kinds of comparisons, because each of them was at top level for 10 or 11 years.
No group has taken responsibility so far.
The latest attack happens after a series of incidents in East Java - Surabaya Police headquarters bombing on Monday, three Surabaya church bombings on Sunday morning and an accidentally blast inside a low-priced apartment in Sidoarjo on Sunday night.
Police shot a militant and arrested at least 13 others in a series of raids following the Surabaya attack.
The attack comes days after over two dozen people were killed in a series of terrorist strikes in Indonesia, including suicide bombings by a family of six in three churches on Sunday in the islands second largest city, Surabaya.
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"Four suspects were killed by police personnel during the attack".
The next day, members of another family blew themselves up at a police station in the city, wounding 10.
State news agency Antara said two journalists who had been at the police headquarters were also hurt in the attack.
Wasisto said the driver has been apprehended and was now being detained at Riau Police Precinct. One ran away but was later captured and taken to the Pekanbaru Police headquarters.
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