Errors included not advertising a call for nominations in a local newspaper and failing to post forms to all potential voters.
The board had been offered the option of running a new election, with ministry support, but declined.
Larry Forbes, who is coming to the end of his two-year tenure at Pamapuria School near Kaitaia, was yesterday appointed commissioner of the kura.
Ms Casey said Mr Forbes would work with the community to set up an advisory group of whanau to guide and support him.
"He will ensure students' learning is disrupted as little as possible while he works with the community to run a new election. Once he takes up the post, he will report back to us on the expected time frame for new elections."
Once a new election had been held, the commissioner was usually able to hand responsibility for governance back to the board.
Mr Forbes had a strong track record of resolving issues at schools and working with communities, she said.
Ms Casey said the ministry only intervened as a last resort. Te Runanganui, the national body representing kura kaupapa, had been fully consulted. The kura's recently-appointed principal would remain in place.
Outgoing board chairman Terry Smith was in Wellington yesterday and could not be contacted for comment.
Ministry intervenes
Eleven Northland schools are under some form of intervention, the Ministry of Education says.
Two have limited statutory managers in place while nine have commissioners, a more drastic form of intervention. Nationally, 60 of New Zealand's 2500 primary and secondary schools are under intervention.
In recent weeks Moerewa School has gone back to being self-governing after a controversial two-year intervention, while Kerikeri Primary and Te Kura Kaupapa Maori o Whangaroa have joined the list of schools run by commissioners, the former after the board of trustees resigned in an apparent bid to force the ministry to intervene.
Schools with limited statutory managers
*Kaikohe Intermediate (since August 2013)
*Omanaia School (September 2013)
Schools with commissioners
*Northland College (since June 2012)
*Kaitaia Abundant Life School (April 2013)
*Kerikeri Primary School (June 2014)
*Ngataki School (October 2013)
*Te Hapua School (September 2013)
*TKKM o Whangaroa (June 2014)
*Pamapuria School (August 2012)
*Poroti School (August 2013)
*Tangowahine School (February 2014)