The said officer, Subhas Kumar Dash, has been at loggerheads with Thampu since last year.
As Thampu suspended Dash last year on charges of engaging in "gross misconduct", the latter had accused the Stephen's principal of forcing him to convert to Christianity.
Also, Dash had earlier this month sent a legal notice to the principal alleging that he was being made to work in a store room at the college.
"Certain things have come to light regarding Dash's functioning at the college, which are criminal in nature. I have lodged a complaint with police to investigate the same," Thampu told PTI.
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"The (St Stephen's) principal had given a complaint against their own administrative officer, which is under investigation at Maurice Nagar police station. No FIR has been registered in the case yet," said DCP (North), Madhur Verma.
Dash was last year suspended by Thampu on charges of being responsible for "gross misconduct" and sending derogatory and defamatory SMSes to the Stephen's administration and the college community under the influence of alcohol.
Dash had thereafter moved Delhi High Court accusing Thampu of forcing him to convert to Christianity. He was reinstated on the college staff last month after he tendered an apology and the issue was settled out of court.