An internal investigation found bosses at North Ayrshire Council broke Scottish Government rules when they made the appointment at Garnock Academy.
Problems came to light following a complaint about the process by the school's parent council, and an investigation found the council broke rules under the Scottish Schools (Parental Involvement) Act 2006.
Parents criticised the job description in the council's advertisement for a new head, calling it 'vague', and also complained about council officials, saying parent council chairman Brent Norris was not impartial in the recruitment process.
The parent council subsequently voted overwhelmingly to reject that accusation by the council.
Mr Norris and colleagues have welcomed the new head, Alan Dick, and promised him their every support.
Mary Docherty, head of service, education and skills, told parents: "I regret very much that we did not engage with the parent council earlier in the process. We've been very negligent and lessons have been learned."
Director of Education Carol Kirk said: "We hold our hands up. There was no intent on our part to exclude the parents at Garnock.
"We want to get the best, most inspirational educator we can for all our schools and we feel we have still done that here."
Meanwhile, Ms Kirk will retire in March.