Local journalist Doddy Vladimir, who was at scene of the attack, said he saw a white Toyota Avanza van hit the headquarter's fence at around 9am (02:00 GMT).
Attack comes after multiple bombings in Surabaya in the past week.
National police spokesman Setyo Wasisto said the men attacked officers after driving a minivan into Riau province's police headquarters.
"Two police officers were wounded in the arms and head by the sharp weapons", Sunarto told Detik.
The alleged driver fled but was later arrested by the Riau Police.
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The attacks are the worst in the world's biggest Muslim-majority country since the bombing of tourist-packed restaurants in Bali in 2005.
SUSPECTED militants carrying swords and a bomb have attacked a police station on the Indonesian island of Sumatra, as Islamists continue to wage war against the south-east Asian nation.
On Monday, a suicide bomb attack outside a police building, carried out by one family and claimed by the Islamic State of Iraq and the Levant (ISIL) group, killed at least 10 people.
Police suspected Sunday's attacks on the churches were carried out by a cell of the ISIL-inspired group Jemaah Ansharut Daulah (JAD).
"People should take care not to be in places where there might be terrorist attacks, to read the advice, to take notice of what local authorities say and to register (with DFAT via Smarttraveller) so the Australian missions overseas know they're in country".
After some major successes tackling Islamist militancy since 2001, Indonesia has seen a resurgence in recent years, including in January 2016 when four suicide bombers and gunmen attacked a shopping area in the capital, Jakarta.