In a report submitted to the High Court on Tuesday, FSA said it also found the presence of cadmium in the samples.
The 11 companies are Milk Vita, Dairy Fresh, Igloo, Farm Fresh, Aftab Milk, Ultra Milk, Aarong, Pran Milk, Ayron, Peura and Sef Brand.
The bench of Justice Nazrul Islam Talukder and Justice KM Hafizul Alam received the report.
Previously, the Bangladesh Standards and Testing Institution (BSTI) claimed to have found harmful ingredients in only two of the 350 samples it had tested.
The court said other countries would slap companies with huge fines if harmful materials were found in their products.
FSA counsel Faridul Alam said they tested 50 liquid milk samples, 11 pasteurised milk samples and cattle fodders of six companies at three government and as many non-government laboratories.
“All milk samples were found to have contained lead and cadmium beyond tolerable level,” he said, adding that the fodders were found to be safe.
Faridul said Dhaka University’s Professor ABM Faruque tested milk against 19 parameters. The BSTI tested samples against nine parameters while the FSA conducted tests against five parameters.
The report says FSA collected 500/1000ml pasteurised milk samples from super shops and sales centres in the city.
The samples were tested at the labs of Bangladesh Agriculture Research Institute, Bangladesh Council of Scientific and Industrial Research, Bangladesh Atomic Energy Commission, Plasma Plus, WAFFEN Research Lab and iccdr,b.
The court ordered BSTI and FSA to inform it within July 28 about legal steps taken by them following the findings of the report.
HC also ordered pharmacies not to sell animal antibiotics without prescription from a veterinarian.
Advocate MR Hasan Mamun stood for BSTI while Deputy Attorney General AKM Aminuddin Manik represented the state.
The court on February 11 issued a rule seeking reports from BSTI and FSA about bacteria, antibiotics in milk, lead in curd and insecticide in cattle fodder.