The board merger idea comes on top of a ministry letter threatening to appoint commissioners to run any school that cannot find enough people to serve on its board.
Moari Taylor from Okaihau's Horeke School, which has two teachers and 28 students, said the merging of boards was worrying.
"We have five nominations for five positions," she said. "We are worried that if they merge boards they are looking at merging schools."
Four schools had failed to fill their boards, Parata said.
One, in Canterbury, has agreed to turn over its governance to a ministry-appointed commissioner.
The education minister said serving three years as a trustee was "a big commitment," but the government valued parental involvement and had nearly doubled the funding for boards in the Budget last week.
The trustee system could be adapted to better reflect 21st century governance, she said.
"But the basic grassroots democracy is a very powerful voice for parents."
Unions and associations representing teachers, principals and trustees gave a mixed response to Parata's merger talk.
Post Primary Teachers' Association president Angela Roberts said school board members needed to have increasingly sophisticated skills to deal with growing financial pressure.
Labour education spokesman Chris Hipkins said high decile schools had no problems finding good board members, but poorer schools struggled.
He was concerned Parata would force their boards to merge.
Voting has started in about 1,300 schools which have enough candidates to hold an election, and results will be declared after the polls close on Thursday.
School Trustees Association general manager Ray Newport said 1,056 of New Zealand's 2,384 state and state-integrated schools - not including 80 Maori schools - had already declared results because no vote was needed.
