Cordons were put in place at the intersection of Otaika Rd and Raumanga Valley Rd and another near Exeter St as well as West End Ave and Te Mai Rd, at the back of Horahora Primary School.
Staff and students at the school were told to stay inside while the incident was unfolding.
Whangarei police spokeswoman Sarah Kennett confirmed four stun grenades were thrown into the house just after 2pm. Following the loud bangs, that echoed around nearby streets, a dog ran off the property.
An ambulance arrived at a cordon as a precaution but left five minutes later.
Mrs Kennett said when police searched the house they did not find the couple and late yesterday officers were trying to track the pair down.
The incident was run by police staff in the new District Command Centre at the Whangarei police station, Mrs Kennett said. They were able to monitor the situation closely and send staff to locations where they were needed.
The command centre has been operating for about two months and works with police communications in Auckland.
Horahora Primary School principal Pat Newman said police were quick to let staff know about the incident and the school went into lockdown.
"We have procedures we follow and they were followed," Mr Newman said.
"All the kids were inside, we pulled the curtains so no one could see in. They were doing their work, oblivious to what was going on outside."
He was concerned some parents ignored school warnings and collected their children from class.