The probe follows a complaint lodged by MP Buddhika Pathirana to the Bribery Commission.
It says the chief accountant, tender board and technical committee chairmen were responsible for the fraud that had taken place in 2017 and 2018.
Six months ago, Hettiarachchi was transferred to the state administration pool, but she refused to accept and remained at the Defence Ministry.
This time, the Public Administration Ministry has warned her that if she disregarded the transfer, she would be considered as having vacated her post.
Pathirana said minister Ranjith Maddumabandara has requested him to give him full details of the fraud, which he would do at the UNP parliamentary group meeting starting at 3.00 pm today (05).