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The US agency, in a letter dated May 8 letter, cites unspecified conditions that are yet to be met by some of the implementing partners.
The letter signed by Brian Woody, the USAid/Kenya and East Africa contracting officer says activities such as salaries and wages, operations, domestic and international travel as well as meetings and workshops have been suspended.
The directive is a major blow for President Uhuru Kenyatta since funding for domestic, international travel and activities undertaken during such trips like training, conferences, site visits and conventions have been suspended.
Other activities the agency will not fund include meetings, events, and workshops as well as the printing of communication material such as brochures, training materials, and guidance documents.
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The directive indicated that any activities conducted with the MoH during the period of suspension will not be reimbursed by the United States Government.
In 2015, USAID distributed 3.8 million mosquito nets in 23 endemic and epidemic counties prone to malaria attacks.
In the same year, the agency signed a Sh65 billion ($650 million) contract with the Kenya Medical Supplies Authority (KEMSA).