"We are investigating it," The Star cited Mr Hisham as saying, adding that he did not want to speculate on the details yet.
In a statement, the FDA said the agency had requested that the Malaysian government "investigate the cause of the residue problem and develop a programme of short-term and long-term actions to prevent the export of violative shrimp from Malaysia to the United States".
The FDA said it was placing companies that process or ship shrimp and prawns from Peninsula Malaysia on "import alert", meaning that their shipments could be detained at the port of entry without physical examination.
Sabah and Sarawak were excluded from the import alert, it added.
The notice said that from Oct 1, 2014 to Sept 30, 2015, the US FDA tested 138 samples of shrimp and prawns from peninsular Malaysia. In all, 45 samples or 32 per cent contained residues of both substances, it said.
Malaysia will ask the FDA for details on its move, Agriculture and Agro-based Industry Minister Ahmad Shabery Cheek said.
Banned from use in seafood farm operations in both Malaysia and the US, nitrofurans and chloramphenicol are antibiotics that help prevent disease in prawns and shrimp but are harmful to humans.
Malaysia is one of the top 10 exporters of prawns and shrimp to the US.
So far, the prawns imported by Singapore appear to be free of the banned antibiotics.
The Agri-Food and Veterinary Authority (AVA) told The Straits Times that it has not detected veterinary drug residues such as nitrofurans and amphenicols in prawns and shrimp from Malaysia.
"Veterinary drugs are not permitted in food, including prawns and shrimp. Affected prawns found to contain veterinary drug residues... would not be allowed to be imported or sold," an AVA spokesman said.
As part of its routine surveillance and inspection programme, imported prawns and shrimp are monitored and sampled for food safety and compliance with AVA's standards and requirements, the authority added. Food products that fail its tests are not allowed to be sold in the Republic.
Last year, Singapore imported 16,400 tonnes of prawns and shrimp, with about 56 per cent or 91,000 tonnes from Malaysia.