The doctor told Bonney, 51, he must stop driving and he is now on leave from his job.
"[The GP's] eyes were getting bigger and bigger," Bonney said. "He said: 'See that here, that ain't supposed to be there.'"
Benign in themselves, arachnoid cysts are removed if they cause neurological problems.
Bonney's vision and balance problems have continued and he said the delay was unacceptable.
Driving 54-tonne trucks, he had inadvertently put the public at risk, he said.
"I've been endangering other road users and myself."
Before the scan, one clinician suggested his problem might be caused by anxiety.
Hearing nothing of the scan result, he thought maybe he was being "paranoid", and should just get on with things.
About four follow-up Dunedin Hospital appointments had been postponed since the scan.
"The hospital kept sending me appointments for a follow-up and then I kept getting another [letter] in the mail. They kept putting it off and off and off."
Shortly after the Otago Daily Times approached the Southern District Health Board for comment on Wednesday, Bonney was contacted and given an ear, nose and throat appointment scheduled for today.
However, the appointment was cancelled yesterday by an ENT specialist who rang Bonney to explain and apologise.
Bonney said the specialist told him the scan result had been transferred to neurology, and had somehow not been followed up.
He appreciated being contacted personally for an apology, but is eager to hear from the neurology department about the next step.
He wants the cyst removed as quickly as possible, and says it is a straightforward procedure.
Health board chief medical officer Dr Nigel Millar confirmed the apology in a statement.
"While we do not wish to comment in detail on individual cases, we can say that we've been in contact with Mr Bonney to discuss his scan and made plans to ensure he gets any necessary care.
"We are also looking into his concerns and will investigate why things did not go according to plan. We have apologised to Mr Bonney and will continue to communicate with him directly."