The consents granted so far have been based on groundwater assessments and modelling, which is based on survey data from the late 1980s and early 90s.
Consents limit the amount of water which can be taken to prevent the intrusion of salt water, which would render the aquifer unusable.
However, new bore surveys carried out by regional council staff have revealed errors in the historic data.
Water levels in the northeastern part of the aquifer, below Houhora, may be 2.5m lower than previously believed, acting chief executive Bruce Howse said.
On the other hand, water levels in the northwestern part, in the Hukatere area, may be 1.8m higher than the old data suggested.
"In a nutshell, this discovery potentially means there's less water available in the northeastern part of the aquifer than previously thought, although there may actually be more available on the northwestern side," Howse said.
The council had already allocated roughly half the water previously presumed to be available in the aquifer's Houhora subzone.
"This potentially means the allocation limit for the northern subzones near Houhora needs to be reduced," he said.
However, monitoring of the aquifer so far indicated existing use was sustainable.
An independent surveyor would be brought in to survey all monitoring bores used to manage the aquifer, and council staff would measure water levels and check water quality in another 60 bores over the next two months.
The council would then need to re-run its water allocation models using the new information.
The current allocation limits, as set out in the council's proposed Regional Plan, may also need to be reviewed.
It was not possible to say what the impact would be on existing consents or new consent applications until the groundwater model was re-run with the new data.
Howse said the council was ''very aware'' of local concerns about the sustainability of the Aupōuri aquifer.
The 17 consents already granted were south of the main area of concern, he said. Stringent conditions included monitoring bores near the coast and inland to keep tabs on water levels and any saltwater intrusion.
The historic inaccuracies came to light while staff were surveying bores to determine the ''trigger points'' at which salt water would start to infiltrate. Their findings were confirmed by Lidar, an laser-based surveying technique.
The current avocado boom is centred on Houhora and Waiharara, where one company alone is planting more than 400ha of former dairy land.
