The three, arrested in an operation on Saturday, were being interrogated by anti-narcotic officials here, Xinhua news agency quoted security sources as saying.
They were linked to a cartel smuggling highly valued cocaine from Brazil and trailed by foreign and local anti-narcotic authorities for months, the sources said.
According to port documents, the containers where teh drugs were found were loaded at Santos Port in Brazil on June 20.
The Port of Mombasa has in the past been used as a transit port for drugs headed to Europe and Asia.
Last year, President Uhuru Kenyatta witnessed the destruction of a ship loaded with heroin valued $13 million.
The vessel was blown up on the high seas as a sign of the government's tough stance against drug trafficking.
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