Otago Rugby Football Union amateur rugby manager Justin Gardner said the club had not got International Rugby Board clearance for two players, who played in Australia last year, to take the field.
Gardner said the metropolitan committee of the union had the ability to strip competition points from the team but had decided to just fine the club.
He said it was important to adhere to IRB regulations, and complete all the proper forms.
Pirates chairman Chris Rowe said the club needed a new halfback in a hurry and was bringing in players who wanted to help out Otago rugby.
There had been a breakdown in the completion of the paperwork, he said.
The players were winger Marshall Suckling and halfback Steve Bruce, who both played on the Gold Coast with Pirates coach Roy Hawker last year.
Rowe said the club was disappointed but would accept the punishment and get on with the rest of the season.
