Committee officials stated recently that students had been "denied study opportunities" and that scholarships had taken a "massive hit" through the cutting of the Step Up, Bonded Merit and Top Achiever doctoral schemes.
Existing scholarship holders are unaffected but future scholarships are being phased out as a result of changes announced in the Budget.
New Zealand Union of Students Associations co-president Sophia Blair said the cuts would have negative effects on tertiary students, and she was also concerned about the lack of consultation with universities and student organisations before cuts were made.
Otago University Students Association president Edwin Darlow said it was "disappointing" to see any tertiary education funding being reduced.
Students were already concerned about overall student debt levels, at present exceeding $10 billion, and adding further debt by reducing scholarship support was undesirable, he said.
The cuts were a "disgusting" development, Otago Polytechnic Students Association acting president Meegan Cloughley, said.
She knew several students who were either receiving support from the Bonded Merit scholarship, or wished to apply for it.
She was concerned that the loss of scholarships would result in some students from modest-income backgrounds being discouraged from pursuing some courses or careers because of the cost.
Dr Charles Tustin, director, graduate research services, at the University of Otago said the loss of the scholarships was "unfortunate", with the phasing out of the Top Achiever scholarships having the greatest significance for Otago University students.
Those scholarships provide an annual stipend of $25,000 a year, and also fund tuition fees for PhD study undertaken either in New Zealand or abroad.
The scholarships were particularly significant not only because of the extent of financial support, but also because of the strong record of success by Otago students in gaining them, he said.
In one recent round last year, 10 of about 40 scholarships allocated nationally had been received by Otago students.
A more positive feature of the Budget was the retaining of domestic-level tuition fees for international students wishing to undertake doctoral study at Otago University and other New Zealand universities.