A Bay of Plenty man accused of beating his infant son and leaving him with extensive brain injuries has been found not guilty by jury in a trial in the High Court at Rotorua.

Robert Haami Boynton, 39, from Matahi Valley, was on trial after being accused of beating his then four-month-old son and his former teenage partner.

Boynton was found not guilty of injuring with intent to cause grievous bodily harm after his son was flown to Starship Hospital with severe brain injuries.

The jury was unable to reach a verdict on the grievous bodily harm charge with reckless disregard for his son's safety, which was added during the trail.

The alleged offending was reported to have taken place between October 1, 2009, and May 19, 2011, when Boynton was accused of slapping, shaking and throwing his infant son two metres onto a thin mattress.

He was also facing numerous others charges, which he has denied, including perverting the course of justice by threatening his former partner, a charge which he has been convicted on.

He was also found not guilty of assaulting this partner Ngarangi Wickliffe.