This emerged in the report by Audit Scotland into the college's management, which said the incident highlighted "wider risks" for the FE sector as a whole (TESS last week).
The report published for the first time the results of an investigation by the FE funding council into allegations of misconduct by Dr Chalmers, which was completed in February last year.
It found that Dr Chalmers had been claiming 25p a mile for travel instead of 9p, with the result that he had to repay pound;2,691 to the college.
He also received pound;7,500 which he should not have for "services" provided to the University of the Highlands and Islands project of which the college is a part.
Dr Chalmers also used a business credit card, which has now been withdrawn.
The college's external auditors, who failed to reveal those payments, have now been forced to change their procedures in respect of the college principal's salary and now review each monthly payroll.
Dr Chalmers and the college board eventually reached a "compromise agreement", which allowed him to escape disciplinary procedures on the grounds of ill-health.
Part of the agreement was that the former principal would repay the money owed to the college within seven days of receiving his pension lump sum. The sums have since been repaid.
Jim Logan, the new principal, issued a frank condemnation of his predecessor, who, he said, had subjected the board to "obfuscation, misinformation and very unprofessional treatment". The college staff had felt "misled, ignored and marginalised".