The director of the Health Systems Research Institute has sought protection from the prime minister after corruption was found in a foreign-funded project.
Somkiat Wattanasirichaigron submitted the letter to the People's Service Centre on Monday.
Dr Somkiat said the Canada-based International Development Research Centre (IDRC), which finances the Thai institute's international research project, recently audited the project's spending and found some irregularities.
He said this lack of transparency happened under the watch of one of his predecessors who is now a close aide to public health minister Somsak Chunharas.
No evidence has been found for past disbursements and Dr Somkiat reported the findings to Mr Somsak, as well as Public Health Minister Rajata Rajatanavin and the deputy prime minister supervising the ministry.
The lack of progress and responses has led to distrust by the international organisation and badly tarnished the country's image, he added.
On Nov 28, a panel was set up to investigate into his actions with an aim to sack him, he said.
"To defend myself, I gave related documents and file petitions with the National Anti-Corruption Commission, the Auditor's General Office and the Public Sector Anti-Corruption Commission. However, I haven't received or seen a formal order," he said.
"I'd like to ask the prime minister to protect me as a whistle blower of this abuse of authority."