A man who spent more than three years in prison after being wrongly convicted of abducting and raping an 11-year-old girl has today been awarded $868,000 in compensation.

Convicted in 1993, David Dougherty was acquitted on retrial in 1997 when it was found DNA evidence left on the girl's clothing could not have come from Mr Dougherty, but belonged to another man.

Mr Dougherty's compensation includes $168,728 for pecuniary losses - for lost income, legal and other costs - and $700,000 for loss of liberty, loss of reputation, loss or interruption of family and other personal relationships, and mental and emotional harm.

Auckland lawyer Stuart Grieve, QC, assessed Mr Dougherty's eligibility for compensation.

Mr Grieve confirmed Mr Dougherty was innocent and recommended that $868,728.80 should be paid to compensate him for the losses and suffering incurred because of a wrongful conviction.

Justice Minister Phil Goff said today that cabinet had accepted Mr Grieve's recommendation.

"Mr Dougherty was entirely innocent of the crime for which he was convicted and imprisoned," Mr Goff said.

"The payment made to him is a practical expression of society's obligation to make up for what he lost and what he has suffered."

Mr Goff said calculations of compensation took into account that no aspect of the investigations carried out by the Police and ESR could be regarded as aggravating or contributing to the wrongful conviction and detention of Mr Dougherty.

He said the convictions were the result of the mistaken identification of Mr Dougherty by the complainant.

The amount paid to Mr Dougherty was reduced to take account of his previous convictions, none of which involved sexual of violent offending.