Two 14-year-old Aboriginal boys have made an official complaint to WA Police after officers in the Pilbara allegedly threatened them with guns.

The boys were among five passengers in a car which pulled over by officers in South Hedland on April 5.

According to the complaint filed by the Aboriginal Legal Service, the police car had been following the vehicle when the driver "panicked" and veered off the road.

When the car became stuck in a ditch, everyone got out and "started running".

Police caught the two 14-year-olds and one other boy, as others hid in bushes or ran away.

The boys allege they were told to "get down" and one of them said he "could feel the officer aiming a gun on the back of his neck".

The officer then allegedly yelled at them to "stop crawling away or I'll shoot you with the gun".

One of the 14-year-olds claimed he was tackled to the ground and hit in the face and ribs before being kicked in the ribs and hit on the leg with a baton.

The complaint letter claims a witness saw the officers aiming a gun, heard them tell the boys to shut up, and used abusive language.

A witness is also alleged to have seen "the officers" hit one of the boys on the "back of his head with their gun".

No charges laid against passengers

The two 14-year-old boys were handcuffed and taken to South Hedland Police Station, where they say they were strip searched and detained.

A third boy was also taken to the station.

No charges were laid against the trio, but they all spent the night in cells.

The driver of the vehicle, who was not detained on the night, was later charged with failing to stop and driving without a valid licence.

He pleaded guilty to the charges and was referred to the Juvenile Justice Team.

The WA Police Internal Affairs Unit has started investigating the complaint, which was filed by the ALS late last month.

The officers remain on full duties while the initial assessment of the complaint is carried out.