Adrian Wall, 49, Liiban Nursharif, 30, and Daud Ali, 40, were held on Tuesday after officers swooped on homes in London, Coventry and Cardiff.
They were arrested under the terrorism act as part of an investigation into the illegal exportation of khat to the US and Canada where it is a controlled substance.
The three men are jointly accused of conspiracy for allegedly mislabelling parcels being sent from the UK.
Married father-of-six Ali, who runs a taxi firm which has contracts with several schools, was also charged with possession of a fake Norwegian passport.
The three defendants spoke only to confirm their names, dates of birth and addresses when they were brought before Westminster Magistrates' Court in central London.
They sat with arms folded during the hour-long hearing where Ali and Nursharif were remanded in custody.
Wall was granted bail subject to restrictions.
The three suspects were among seven people arrested by officers investigating a network suspected of funding terrorism at the Met's counter-terrorism command during a pre-planned, intelligence-led operation earlier this week.
The remaining four suspects - a woman aged 45 and three men aged 47, 45 and 42 - continue to be held under the terrorism act, Scotland Yard said.
Homeland Security Investigations in America and officers from the UK's counter terrorism network, the UK Border Agency and local forces were also involved in the operation.
Wall, a married father of four of Pitt Road, Thornton Heath, Surrey; Nursharif, a single man of no fixed abode and Ali, of Wakehurst Place, Cardiff, will next appear at Southwark Crown Court for a plea and case management hearing on July 6.