Toy giant cites choking and lead poisoning risks in second safety warning in two weeks.
It did not say where the Colgate toothpaste had been produced.
The order followed a spate of scares in the United States and several other countries about the safety of Chinese products, including seafood found to contain antibiotics, and toothpaste containing toxic chemicals imported from China.
Mattel, the largest US toy company, has recalled about 20 million Chinese-made toys because of the danger from lead paint and small magnets which may become detached.
The Nigerian agency said it would punish dealers who did not dispose of all foreign-made toothpaste because it was not registered for use in Nigeria and its safety could not be guaranteed.
“All importers, distributors and marketers of imported toothpastes are directed to submit them to the nearest NAFDAC office for destruction or face serious sanctions,” the agency said.
No one is known to have fallen ill after using foreign-made toothpaste in the country of 140 million.
NAFDAC began a crackdown on counterfeit products in 2001 after many years as a dumping ground for ineffective and often dangerous drugs and other items.