The cases were filed at Gulshan, Dhanmondi, Ramna and Uttara police stations on Saturday, the directorate said in a media release.
The Customs also recommended anti-corruption commission to take necessary steps to start an investigation.
Brothers Dildar Ahmed, Gulzar Ahmed and Azad Ahmed, who own the Apan Jewellers, are made accused in the cases.
The charges against them include hiding information of those ornaments in tax statements. The customs brought the charge under the Money Laundering Prevention Act.
The owners of Apan Jewellers are facing five other cases initiated by the Dhaka Customs House under the Customs Act on charges of depositing smuggled gold.
Besides these case, the National Board of Revenue recommended action by the Anti-Corruption Commission on charges of availing assets beyond the known sources of income, the release said.
Customs detectives raided five Apan Jewellers outlets and seized the gold after the owners failed to show valid procurement documents.
The ornaments were apparently made from smuggled goods, CIID chief Moinul Khan had told bdnews24.com at the time.
One of the owners, Dildar, is the father of Shafat Ahmed who has been arrested on the charge of raping two university girls at a hotel in Banani. Four others, co-accused in the rape case, are also behind bars.