The New Zealand Association of Scientists (NZAS) has now contended the financial motivation for the changes, citing documents released under the Official Information Act that indicate the college's profit was actually $11.7m higher than Massey first predicted.
Financial information provided in the first discussion document stated the college would have a "contribution deficit" of approximately $15.7m in 2020.
The released documents also suggested Massey's School of Natural and Computational Sciences - now to be split between the two new schools from next year - returned profits of more than 30 per cent over each of the last three years.
The NZAS further questioned how Massey calculated its target student-to-staff ratio, and said that while the university had provided an explanation of the ratio, it hadn't disclosed the workings behind the target.
In a statement emailed to the Herald, the association argued the figures showed teaching was not the source of financial problems at the college.
"It seems that Massey University is compromising its academic offerings for no good reason and wasting public money by restructuring a school that has been academically and financially successful."
Tertiary Education Union organiser Heather Warren said the union agreed with members' concerns that there'd been "little effort" put into creating a business case based on the financial position of the college.
But the TEU also recognised there were other factors outside of college finances that were being considered, she added.
In response to an email laying out the NZAS concerns around finances, a Massey spokesperson said each of the points needed to be "read in the context of the documents in which they were published".
The spokesperson said the latest announcement confirming the new schools also wasn't Massey's final decision on the college restructure, and wasn't based on any financial consideration.
Rather, they said, it was based on "the most sensible arrangement of similar teaching and research subject areas such that students and other stakeholders to the university can intuitively find the qualifications, staff or resources they are looking for".
The changes would see biological and physical sciences disciplines grouped into one school, and mathematics, statistics, computer science and information technology into another, with both spanning Massey's Auckland and Manawatū campuses.
Reporting lines, meanwhile, would shift to the heads of each new school, who were still to be appointed.
The positions of head and deputy head of Massey's current School for Fundamental Sciences and School of Natural and Computational Sciences would be disestablished by the end of the year, with the incumbents to continue in their substantive roles.
In his decision sent to staff, the college's pro vice-chancellor Professor Ray Geor said there were no plans for changes in physical working arrangements for staff at this stage, beyond some transfers from Albany's Ōtehā Rohe campus, and Manawatū's Vet Tower.
But he added working groups planning the new schools would be asked "to consider if such opportunities exist", taking into account the advantages and disadvantages involved.
Geor thanked staff for their feedback, and acknowledged the uncertainties the process created, "especially with respect to the implementation of the new schools and also ensuring strong and effective leadership of schools that span campus".
One senior Massey academic however remained sceptical about the changes.
"We have lost so many people and majors at this point that morale has sank to the point where these new changes just wash over us."