Chikwe Ihekweazu, the director general of the NCDC, said they had found evidence that the lab was collecting samples and money from unsuspecting travellers, but failing to test them.
Instead, they issued certificates claiming they had tested negative for the virus, enabling them to travel.
Mr Ihekweazu added during the organisation’s weekly briefing on Monday that a full list of accredited labs was available on the NCDC’s website and encouraged members of the public to only get tested at those centres.
He said that they were working on a platform where every lab in Nigeria could publish their test results which could then be easily verified by airlines or other countries wishing to check whether a result was genuine.
He did not specify when this platform would be ready.
The authorities in Nigeria recently suspended flights from the Emirates airline because the carrier wanted passengers from Nigeria to take a rapid Covid-19 test four hours before flying, in addition to the standard polymerase chain reaction (PCR) test.