The government's non-governmental organisation (NGO) coordination board said in a statement it had "de-registered 510 organisations for non-compliance with the law", with some using their charitable status as a front for raising cash for terrorism.
"Some NGOs have been and continue to be used for criminal activities, including as conduits of terrorism financing in Kenya and in the Horn of Africa," the statement read, which did not specify the names of such groups.
From the names of 510 listed, many appeared to be aid agencies and charities, with many closed for failing to provide financial audit returns.
"The board has with immediate effect de-registered these organisations, frozen their bank accounts and forwarded information on them to relevant government security agencies for immediate action," it said.
Kenya's government has been under fire since last year's attack by Somalia's Al-Qaeda-affiliated Shebab on the Westgate shopping mall in Nairobi, in which at least 67 people were killed.
Earlier this month Kenya's interior minister and police chief were removed from their posts after the Shebab carried out massacres in the northeast of the country.
The organisations were identified "in collaboration with security agencies both locally and internationally", the statement added, without giving further details.
Kenyan lawmakers are currently deliberating proposals to boost security laws, criticised by some as being too tough and restricting freedoms.
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