The employees, represented by two unions — the New Zealand Educational Institute Te Riu Roa (NZEI) and the Public Service Association (PSA) — walked off the job from 10am until noon yesterday.
They marched from the Dunedin ministry office in Moray Pl to the Octagon, where they rallied.
NZEI member and speech therapist Amberleigh Stenhouse said she and her colleagues were protesting because the collective agreement offer they received "failed to address key issues raised around workload and staffing issues".
"We were offered a 0% pay increase and a removal of clauses protecting flexible working arrangements and protecting us against restructuring," Ms Stenhouse said.
The offer from the ministry was declined, and a subsequent offer was then made which still included the removal of protections, but offered raises to "just those at the very top".
"We knew it was going to be a tough negotiation space, but we weren’t expecting less than nothing."

They would be working only their contracted hours, taking full breaks, would not be picking up any additional work, no new cases would be started and no children would be taken off waiting lists.
At the protest were service managers, behaviour and communication support workers, field staff, speech-language therapists, early intervention teachers, occupational therapists, psychologists, kaitakawaenga (mediators), advisers on deaf children and service managers.
Similar protests were held around the country yesterday.
The Education Ministry’s hautū (leader) corporate Rob Campbell told RNZ the ministry was focused on maintaining day-to-day operations and minimising disruption to children, young people and their families.
"While we are disappointed that NZEI and PSA have chosen to proceed with industrial action despite initial offers, we remain committed to progressing collective agreements in good faith with the unions," he said.