Taxis to and from school for some special-needs students are paid for by the ministry.
At the end of last year, it put the contracts out for tender and changed providers in areas including Whangarei, the North Shore, central Auckland, South Auckland and Tauranga.
Resulting problems were widespread and included students being picked up late or not at all.
The principal of Mt Richmond School in Otahuhu, Kathy Dooley, said the ministry had paid for an administrative assistant at the school to sort out what she dubbed the "taxi version of Novopay".
She also expects to be reimbursed for the thousands of dollars she spent hiring South Auckland Taxi drivers after problems with Co-op.
"Let's hope that this will work, and let's hope that we don't go back to square one again."
The ministry has also had to bring in another provider, R&R Total Mobility, to help Alert Taxis cope with school runs in North Auckland. It would not reveal what it was paying.
Those steps have seen problems at most schools settle down; however, some persist.
Jan Kennington, principal of Takapuna-based Wilson School, said she believed drivers were not paid enough to do the jobs, meaning many did not want to be doing the work.
School trek much easier
Keegan Lewis has settled into his new school - but just as important for his family is that he now has a way of getting there and back.
The 17-year-old, who has severe cerebral palsy, autism and epilepsy, started at Northcote College this year.
When the Herald last spoke to his mother, Franky Lewis, she was battling the Ministry of Education to get taxi transport approved for Keegan's journey to and from their Whangaparaoa home.
The taxis have now been approved - temporarily- and Keegan is free to get on and enjoy school life, Ms Lewis says. A long-term solution is being discussed.