Regional harbourmaster Chris Bredenbeck said it was important to get the markers back in place.
"We had a number of buoys that had been lifted up by the currents and dragged into and around the harbours by the surges. Whitianga and Tairua are popular harbours, especially at this time of year, so it was important we got out there to relocate the channel markers as soon as we could."
Maritime officers in three vessels surveyed the locations of the channel markers within the harbours and returned those that had moved back to their correct positions.
"There have been a lot of extremely unusual currents running over the last couple of days and we're fortunate that we didn't get the same destructive impacts as up north," Bredenbeck said.
A red lateral port marker and a yellow 5 knot speed marker that mark the entrance to Whitianga harbour were expected to be recovered from the middle of the bay off Brophys Beach in Whitianga this week.
Bredenbeck urged boaties to remain extra vigilant when navigating the waterways.
Anyone who notices navigational hazards or buoys that are not where they should be is asked to contact the Harbourmaster's Office on 0800 800 402.