The official was arrested after being interrogated along with two of his colleagues, CBI officials said, but declined to divulge further details.
Earlier in the day, CBI said three customs personnel had been detained for questioning in connection with the case.
CBI, investigating the case related to missing of the gold seized from smugglers and kept at the customs office here, had last month arrested two Customs department officials, who have since been suspended.
However, as per the present estimate 34 kgs of gold and foreign currency equivalent to about Rs 17 lakh were missing.
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The investigating agency said the exact figure could be arrived at only after final verification of accounts (of gold seized).
But some of the vital documents to cross examine the amount of gold stored in the strong room as well as the amount of gold handed over to the owners who paid the required duty were missing, CBI said.