He stood down from the board on February 1, 2016, telling Fairfax Media later he had done so because he had been part of an attempt to buy Stonewood before receivers were called in and he considered he had a conflict of interest.
The company was placed in receivership on February 22, 2016, owing unsecured creditors $15million, and it is now being liquidated.
Asked if he could rule out action against Boult, Cain said: "No".
He could not give an assurance the investigation would be completed before the local body elections on October 8.
"It's really hard to pick. We're not running this investigation to the timetable of the local body elections."
Cain said funding of the investigation had just been secured and it would be carried out by "a team of people" at Ernst and Young.
In an email to the Otago Daily Times late yesterday, Boult said he welcomed the investigation, which was normal practice for a liquidator.
"My duties as a director were carried out with care and diligence.
"I always acted in the best interests of the company to implement a solution that was intended to be beneficial to the creditors and the major shareholder.
"Ultimately the sole shareholder who controlled the company decided the outcome.
"At that time I had no option but to resign."
Boult said he was involved in a group that looked at a potential buyout of Stonewood, but that did not eventuate.
"I remain confident in my bid to represent the residents and ratepayers of Queenstown Lakes district as their mayor."
Cain said he would not like to make a guess at how long the investigation would take "and I also would not like to make a guess as to what the likely outcome is either".
"There's a lot of information to get through and we can't rule out any outcome at the moment."
Cain said depending on what the investigators found, "matters" could be referred on to other agencies or legal proceedings "in the company name" could be taken against individuals.