The sources said the private company employees allegedly acted in collusion with officials of customs officers for the duty waiver and paid a bribe of Rs. 25 lakh in this regard.
Premises of a superintendent level officer of customs were also searched by the agency, they said.
The agency has refused to name the accused as searches are still on.
The premises of private company's executives were also searched in Mumbai, Punjab and national Capital in this regard, they said.