More than 180 union members who work at NIWA have lodged personal grievance claims against their employer, saying they are being denied access to health insurance that was given to non-union staff.
But the the National Institute of Water and Atmospheric Research says an offer of free medical insurance to union members was part of ongoing talks for a collective agreement.
A NIWA spokesperson said staff on individual employment agreements last year accepted an offer of a six percent pay rise and free health insurance.
They said the same offer was made to staff who were Public Service Association (PSA) members, but the collective agreement had not been settled.
PSA national secretary Duane Leo said NIWA's stance discriminated against union members and subjected them to unnecessary pressure and stress.
"NIWA said in September that the health insurance was a well-being policy offered to all permanent staff. However, when union members accepted the offer, NIWA refused to give it to them in an attempt to undermine the PSA's position," he said.
Collective bargaining at NIWA began in August last year.
"It's deeply disappointing that NIWA would try and use staff well-being as some sort of bargaining chip," said Leo.
He said NIWA's stance had caused a great deal of anxiety for members.
"We know of members who have delayed surgery or other medical treatment hoping the issue of the medical insurance would be resolved."
Leo said as well as members lodging personal grievance claims, the PSA had taken legal action against NIWA. The case, which had been filed in the Employment Relations Authority, would be the subject of mediation this week.
NIWA said it remained committed to a joint PSA/NIWA working party established in 2022 to identify and address any gender pay equity issues.
"Given NIWA employees are amongst the higher paid within the New Zealand science system, NIWA believes that in the current environment the offer of a six percent salary increase and free health insurance is a very good one," said the spokesperson.