Sanjeev Kumar, currently serving at the Excise Department's Kundli division in Haryana's Sonipat, was arrested three days ago after his day-long questioning by the Central Bureau of Investigation (CBI) officials in New Delhi.
He was later presented before a special CBI court in the city that sent him to the agency's custody till May 28.
Mr Kumar is accused of stealing a 100 kg gold from the custom's godown at IGI Airport where he was posted as custodian between 2002 and 2004.
The CBI took over the case from the Delhi Police and filed an FIR on March 17.
"In the case, it has so far found that the 100 kg of gold was pilfered or stolen and replaced with non-precious metal in the custom's godown," the CBI official said.
He said that the agency also conducted searches at his residential premises in Delhi a day after his arrest and recovered some incriminating documents.