Hooker Mathew Mullany took the field last week as a replacement for Harbour at Hancock Park in contravention of metropolitan committee rules after having played for Zingari-Richmond earlier in the season.
Otago Rugby Football Union rugby operations co-ordinator Richard Perkins said the transfer of the player had not been completed.
The metropolitan committee met on Thursday and decided to dock Harbour the competition point it earned for the 21-19 loss. It will also lose the 19 points it scored.
Mullany started the season playing for Zingari-Richmond but left that club to play for Harbour.
Under metropolitan committee rules, after the fourth week of the season, any player who switches clubs has to stand down for two weeks.
By taking the field last Saturday, Mullany broke the two-week rule.
Perkins said the rule had been set up to stop players switching clubs at the drop of a hat.
Mullany would not be able to play for Harbour today but could turn out next week.
Perkins said it was rare for clubs to be docked points, and he could not remember the last time it had occurred.
Harbour premier coach Jack Medder said the club would accept the penalty, and it just wanted to get on with the season.
He said there appeared to be a misunderstanding over the clearance, but there was no doubt the club was at fault, even though it had not actively recruited the player.
The two-week stand-down should be brought forward and come into effect after three weeks, he said.
Zingari-Richmond chairman Murray Collie said he did not have an issue with Harbour, and felt the clubs had been let down by the player.
He said the relationship between the two clubs, which battle for the Scoles Memorial every year, was healthy.
The Pirates Colts division two side has withdrawn from the competition because of insufficient player numbers.
