"We have halted their operations," said Steve Okello, the chairperson of the NGO Board, the state-run body that oversees all charities in the country.
The NGOs affected include charities whose work defending the rights of political activists and people affected by a crude oil production project in western Uganda has irritated some government officials.
President Yoweri Museveni's government has been increasing pressure on NGOs, accusing some of them of backing the opposition.
Last December, police detained a government critic and the head of Chapter Four Uganda, one of the NGOs suspended on Friday, on money laundering allegations.
The organisation dismissed the accusations, saying the arrest was part of a crackdown on dissent before elections next month.
Museveni, who has ruled the east African country since 1986, has long been accused by some Western governments, international pressure groups and local opposition of using security forces to intimidate and harass opponents, critics and rights activists.
The NGO Board said Chapter Four Uganda, and other NGOs which it said it had suspended indefinitely, had failed to file annual returns and audited books of accounts. The NGOs did not immediately comment.
Chapter Four is a civil liberties watchdog that has often helped defend leaders and supporters of opposition parties detained on politically related charges.
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