The NGOs Co-ordination Board has banned operations of Kura Yangu Sauti Yangu and We The People for allegedly receiving Sh36 million from the George Soros Foundation.
The two are accused of opening and operating illegal accounts with both NIC Bank and Citi Bank, said to be for purposes of funding political and criminal operations in Kenya.
Executive Director of the NGOs Co-ordination Board Fazul Mahamed in a letter claimed both entities whose activities are supposed to be charitable have employed foreigners contrary to law.
In the letter copied to KHRC, International Commission of Jurists and International Centre for Policy and Conflict, Mr Mahamed directed the two to stop all political operations and election-related programme.
Mr Soros, an American, is perhaps the most feared billionaire world over during election period.
He is a key financier of human rights groups and pro-democracy activists and as a result rubs various governments in the wrong way.
In mid-August, the NGO Board ordered the Kenya Human Rights Commission and the African Centre for Open Governance shut down, but the State suspended the directive for 90 days.