The National Agency for Food and Drug Administration and Control (NAFDAC) has announced the shutting of three firms for failing to fully co-operate with its inspectors.
The companies have not yet commented.
The BBC investigation showed that the syrup was being sold on the black market, and was being used by young Nigerians to get high.
It recorded figures in the pharmaceutical industry selling the drug illegally.
NAFDAC Director Mojisola Adeyeye announced in statement that Peace Standard Pharmaceuticals, Bioraj Pharmaceuticals and Emzor Pharmaceuticals were shut because of “apparent resistance to provide needed documents during our inspection”.
The firms could reopen at a later date, depending on “the level of co-operation that is shown during the comprehensive investigation” by NAFDAC, the statement added.
The agency banned the production and import of cough syrup containing codeine on May 1, 2018.
The ban came the day after the BBC’s undercover team caught one executive for Emzor Pharmaceuticals boasting he could sell “one million cartons” in a week on the black market.
Emzor denied links to the black market and said it had dismissed the employee and launched a full investigation.
Bioraj Pharmaceuticals also denied any wrongdoing, saying it only sold cough syrup legally and said it had suspended an employee and launched an investigation.
Peace Standard Pharmaceuticals denied that its pharmacist showed undercover BBC reporters how to subvert the system and insisted it only supply accredited outlets.
The addictive cough syrup was legal, but it was against the law to sell it to people without a doctor’s prescription or those who did not have a pharmaceutical licence.
The Nigerian Senate estimates that as many as three million bottles of codeine syrup are drunk every single day in just two states, Kano and Jigawa states.