The widow of slain Manawatu farmer Scott Guy ran screaming from the courtroom moments after a jury found Ewen Macdonald not guilty of the 2010 murder, while Macdonald himself broke down in the dock.

The 11-member jury returned its verdict at Macdonald's trial in the High Court at Wellington on Tuesday afternoon following 12 hours of deliberations.

Macdonald - Mr Guy's brother-in-law - stood anxiously in the dock, his parents and brother behind him in the public gallery, as the packed courtroom awaited the verdict.

On the other side of the gallery sat Mr Guy's parents and siblings - including his sister, Macdonald's wife Anna.

Macdonald bowed his head and cried as the verdict was announced.

Moments later, Mr Guy's wife Kylee - who was sitting with his family - screamed "you killed my husband" and rushed crying from the courtroom, quickly followed by other members of both families.

Macdonald was led back to the cells crying as the jury was discharged and the court was briefly adjourned.

A short time later, Justice Simon France remanded Macdonald in custody to reappear in the Palmerston North District Court on July 31.

Macdonald is yet to be sentenced for an arson and criminal damage to two houses on Mr Guy's property in late 2008 and early 2009, and for stealing deer from a neighbour's farm in 2006 - all of which he admitted shortly before being charged with the murder.

Mr Guy, 31, was shot dead in the driveway of his Aorangi Road home, near Feilding, early on the morning of July 8, 2010.

Macdonald - who was a pallbearer at Mr Guy's funeral - was arrested nine months later after a number of appeals from police and the Guy family for help to solve the widely-publicised whodunit case.

The prosecution had alleged Macdonald was angry about his future in the Guy family farm, and wore diving boots with a distinctive sole to carry out the murder, possibly using a shotgun belonging to Mr Guy's father, Bryan.

They alleged he rode a push bike from his home, also on Aorangi Road, to Mr Guy's house, shot him about 4.43am and stole three puppies from Mr Guy's property to make the killing look like a burglary gone wrong.

But Macdonald's defence said the evidence was not strong enough to convict Macdonald, and pointed to someone else being responsible for the murder.

Defence lawyer Greg King said it would not have been possible for Macdonald to carry out the crime within the timeframe the Crown alleged.

Macdonald's family would not comment outside court.

Mr Guy's family says the acquittal leaves them with mixed emotions, and they are no closer to knowing who killed him.

Mr Guy's father Bryan told media outside court they were relieved the trial was over.

The family had been living in the national spotlight during the trial and they wanted privacy to rebuild their lives, he said.

Police, following their nine-month homicide investigation, say they accept the jury's verdict.

They put the strongest evidence they could in front of the jury following a "thorough and professional" investigation, said Detective Inspector Sue Schwalger.