Goa Congress spokesman Sunil Kawathankar, in the complaint, accused Naik of "corruption", "manipulation" and "favouritism" in the recruitment of line helpers in the Power Department.
Naik has rubbished the charges and said he is ready for any inquiry.
"All procedures were followed in the recruitment. I am open for any inquiry," he said.
"The department is in the process of issuing offers of appointment for 646 posts of line helpers in the department. The entire method adopted for filling up the posts is criminally violative of the rules of business of the state government," the complaint read.
The complainant also named a few officials from the Power Department. The main opposition party had earlier moved the Lokayukta against the minister.
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