The original result of the match has now become void and a 3-0 win will instead be awarded to Wanderers SC.
"When finalising the reporting of all match results, as is standard practice after each round in the competition, it was discovered that one of the players was not registered with the club," said Chris Kemp, competitions and events manager for New Zealand Football.
"The club was contacted regarding the situation and it was established that his transfer from a previous club had not been properly concluded. It is an unfortunate situation but if the regulations are breached then we have no option but to impose a sanction."
The deduction of the points from the Wanderers game means Hawke's Bay now have 11 points and drop from second to fifth on the ASB Premiership table. Wanderers remain at the foot of the table.
"To lose the three points at this stage is devastating but the rules are the rules, no matter how unintentional the indiscretion was," Hawke's Bay United general manager John McGifford said.