A terse statement issued on Monday of last week said that James Logan had left that day "by mutual consent". But it emerged later that Dr Logan had decided to step down on health grounds.
The brevity of the statement, which did not mention Dr Logan's health problems, gave rise to suspicions about the reason for his resignation. But he then discussed his illness openly in an interview with the Elgin weekly, the Northern Scot.
He said he had been diagnosed with Horner's syndrome, a condition that affects his eyes, and is due to undergo further hospital tests. Dr Logan is confident he will ultimately be given the all-clear to continue working, but the decision to resign was the correct one.
"Hopefully the outcome of the tests will be positive but, if they are not, I didn't want to be in the position of lingering on as principal. The college needs clear and positive leadership."
The official statement said: "The board of management acknowledges the commitment and enthusiasm of Dr Logan to have the college recognised as a college of the community. The board appreciates his hard work and endeavours in moving towards financial recovery and in the academic development of the college. The college wishes Dr Logan success in his future career."
Mike Devenney, deputy principal, is acting principal until a successor is appointed.
Dr Logan, aged 56, came to Moray four years ago from his position as dean of the school of health sciences at Wolverhampton University, a higher education institution which commended him to a board of management keen to play a stronger part in the University of the Highlands and Islands project.
He took over at a turbulent time when the college was facing a pound;2 million deficit. The former principal had been suspended pending an investigation into financial irregularities at the college and then resigned after being diagnosed with cancer. Dr Logan was quickly catapulted into inquiries by the Auditor General for Scotland and by the parliamentary audit committee.
The new principal told his board on appointment that his ambition was to go "from strength to strength with sound finances".
But, while Dr Logan is credited with stabilising the college, tensions soon appeared as he tried to drive through a redundancy programme. Four members of staff have already gone and another two are due to depart in April.