The letter was signed by current and past presidents of the NZ Association of Scientists (NZAS), the NZ Ecological Society, the NZ Institute of Physics, the NZ Institute of Chemistry, the NZ Mathematics Society, the NZ Plant Protection Society and the NZ Institute of Agriculture and Horticultural Science.
"Massey's proposal and processes undermine all five elements defining a university under the New Zealand legislation," NZAS president Professor Troy Baisden said.
The scientists also argued the threshold for a minister stepping in, while high, had now been crossed.
According to a Parliamentary report, Hipkins would only be able to intervene in the operational or management decisions of a tertiary education institute if its decisions were "inconsistent with the nature of its services, the efficient use of national resources, the national interest, or the demands of accountability".
The scientists further accused Massey's executive as acting with "less accountability than a publicly traded corporation".
"Unless Massey University undertakes immediate remediation of its processes as we request, we call on the Minister of Tertiary Education and the Minister of Research Science and Technology to urgently call in the pace of decision-making at Massey University and install an appropriate independent review mechanism."
Tertiary Education Union organiser Heather Warren said there was a strong view among its affected members that the Government should act.
"Our members are just really distraught and they're exhausted," she said.
"The general feel is that [they're] just completely disappointed in the proposal that has been put to them."
Earlier this month, Hipkins told the Herald issues to do with staffing were decisions for the university - and a restructure for any reason was "clearly" the vice-chancellor's own business to manage.
"As the Minister of Education, it would be inappropriate for me to be involved in operational decisions at universities," he said.
"I would, however, note that the cost-cutting measures proposed are significant. I would expect the university to consult with staff and students before proceeding with any restructures."
When contacted again in light of today's letter, a spokesperson said: "As the Minister has previously said, universities are autonomous institutions and it would be inappropriate for him (as Minister of Education) to be involved in their operational decisions."
A spokesperson for Woods said the minister wouldn't be commenting, saying "it's an operational matter for Massey".
A Massey spokesperson said the university was "committed to working and engaging with staff, students and stakeholders" and that feedback would be reviewed, and suggestions welcomed.
"This is an operational process the university is working through and while this process is underway, and no decisions have yet been made, we cannot make any comment about potential outcomes."
However, Massey did not believe the process was in breach of the Education Act, the spokesperson said.
Today's letter comes after a strained and stressful year for Massey scientists, who learned of the planned shake-up on the first day of semester.
At that point, Massey signalled a need to cut spending by $18.1m a year - including slashing staff costs in the College of Sciences by $11.7m.
In the latest discussion document, the college's pro-Vice Chancellor, Professor Ray Geor, told staff costs had become greater than income, and the situation would "continue to deteriorate unless we take action".
"It is clear that whatever we do to our curriculum we are going to face reducing the number of staff positions over a one-to-two-year period, beginning next year," he said.
"Whilst we wish this was not the case, we simply cannot avoid this reality. My preference is that we recognise the situation and proactively plan to change our curriculum to one that best fits our ability to fund staff positions to deliver teaching and research."
Geor said the document was "not a proposal for change" and any potential changes would go through a separate consultation process.
