Special judge A Bhattacharjee sent Deka to judicial custody after the completion of his 14-day police remand.
Deka has applied for bail and the plea will be considered on Monday.
He had on November 12 surrendered to the police after evading arrest for some days in connection with his alleged role in the cash-for-job scam in the APSC.
Police have arrested 23 out of the identified 25 officials of the 2015 batch who had bribed APSC officials to get jobs through doctored answer scripts.
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Police had on November 8 arrested 16 civil services officials in connection with the cash-for-job scam in the tainted APSC.
Rakesh Kumar Paul, former chairman of the APSC, was nabbed on November 4 last year.
Two members of the commission, Samedur Rahman and Basanta Kumar Doley, and Pabitra Kaibarta, the APSC's assistant controller of examinations, were also held.
Subsequently, more officials and persons were arrested in connection with the job scam.
Nilamani Sen Deka was the agriculture minister in the erstwhile Congress government and had unsuccessfully contested the assembly elections from the Dharampur constituency in 2016.