His department recognised the right of students to hold non-violent protests, he said on Thursday.
Nzimande’s call follows a wave of protests on campuses around the country by students unhappy with the National Student Financial Aid Scheme.
The minister said he hoped meetings between his department and stakeholders would help sort out the problem.
“I also wish to strongly condemn any disruptions and destruction of property, and urge all to desist from this,” he told reporters in Pretoria.
Nzimande said he was concerned about the disruption of lectures, which was causing problems for new students and their parents.
His office would continue to monitor the situation, and would help institutions, students and parents.
He further called on universities to treat students with dignity and respect, and to provide the necessary support in dealing with registration and financial assistance.
“We urge all stakeholders to constructively engage with each other to ensure a smooth registration process. We must not allow the challenges we face to negatively affect the registration process,” he said.
He appealed to students to use strikes and demonstrations as a last resort.