Guido D'Isidoro was suspended on full pay for breaching a confidentiality clause in his contract by publishing accusations against Llandrillo College management on the computer network.
In a letter issued to all staff on the college e-mail system, the staff development co-ordinator claimed that the concentration of power in principal Huw Evans and his deputy and wife Gill left the administration vulnerable to abuse.
In a twist which will alarm other potential whistleblowers in other colleges, a letter from Mr D'Isidoro to Welsh Office minister Peter Hain, found its way back to the college governors.
It is the latest in a series of accusations against managers, which include the case of Doncaster College where the head of personnel is the wife of principal Terry Ashurst.
At both Llandrillo and Doncaster the governors insisted that there were rigorous checks and that extreme care was taken to avoid abuse. But the Association of Colleges said it underlined the need for every college to draft a clear policy on whistle-blowing.
Chris Jackson, chair of finance on Llandrillo College governing body, said: "Mr D'Isidoro's claims have been dealt with comprehensively and independently by the accountants Price Waterhouse. They do not stand up."
The AOC recently issued a whistleblower's charter which says staff should be able to issue complaints internally without fear of discipline or dismissal.
Mr Jackson said: "We do follow these guidelines but Mr D'Isidoro did not complain to us first before going outside the college." The college was, however, considering its own policy on whistleblowing to avoid any uncertainties, he added.
"Regardless of the rights and wrongs, this sort of accusation makes you look even more closely at the workings of the college."
Mr D'Isidoro refused to comment on the case, on the advice of lecturers' union NATFHE.
Neither the college management nor Mr D'Isidoro was willing to give any further details of the claims made against Mr and Mrs Evans before his case is investigated.
Peter Hain said he was unable to comment on how the letter got from his office to the governors without Mr D'Isidoro being contacted. "I will look into it," he said.
It appears that the letter was passed to the Welsh Office officials and on to the Further Education Funding Council. The letter in turn was passed to the governors who were asked to launch a proper investigation.