USAID on Monday issued a notice to suspend funding for activities carried out by a number of Ministry of Health departments.
The US agency,
in a May 8 letter, cites unspecified conditions that are yet to be met by some of the implementing partners.
However, funding for procurement of commodities and equipment related to life-saving treatment, prevention, outbreak or emergency response have been exempted.
Brian Woody, USAID Kenya and East Africa Contracting Officer, listed activities that directly strengthen county health systems will still be funded.
"Surveillance and service delivery will also continue receiving donor cash from USAID," he said.
The suspension will see salaries and wages for project coordinators, administrative staff, accountants, supply chain officers, financial officers, field epidemiology and laboratory training program staff cut.
"If your organisation is directly impacted by this suspension you will receive a separate letter suspending activities and assistance to the MoH."
"However, whether you receive a separate letter or not, you are to refrain from any activities further specified in this letter and inform your contracting or agreement officer immediately," Woody said.
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.
Woody, however, said that clinic data collection tools and national guidelines may be exempted from the suspension.
"Please contact your COR/AOR prior to conducting any of these activities," he said.
Other key departments affected by the suspension order include ICT, security services, building and equipment maintenance, fleet maintenance and fuel.
"USAID will host an information session on Wednesday in order to address any questions or requests for clarifications related to this suspension notice," Woody said.
Woody did not give specific reasons for the mass suspensions although the move could likely be in line with US President Donald Trump's proposal to cut aid.
In the Ministry of Health, US deals with interventions on nutrition, family planning, and maternal and child health, malaria, tuberculosis, HIV/AIDS and strengthening health programs.
There are also programs aimed at making devolution work for the benefit of all Kenyans through democracy, governance and conflict programs.
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).
This increased the amount of US-funded medical commodities it procures, warehouses and distributes.