According to a report in The Star, an intergovernmental committee at the President's office has been calling the shots when it comes to key County appointments, awarding of contracts and deciding which projects should be undertaken.
State House has allegedly seconded individuals to the County Executive Committee (CEC) positions.
Among them is Peter Kariuki, the Nairobi County Secretary, who was formerly the head of President Uhuru Kenyatta's Project Delivery Unit (PDU).
The report further claims that at a November 8 meeting attended by Cabinet Secretaries and County officials, President Kenyatta told Sonko to let Igathe handle the running of the county's affairs while he (Sonko) focuses his efforts on city politics.
The launch of the Sh17 Billion Nairobi Regeneration Project was announced immediately after the meeting.
Deputy Governor Igathe and Tourism CS Najib Balala were appointed Co-Chairmen of the technical committee of the Special Taskforce on Nairobi, the body tasked with overseeing the project.
A statement released by the President read in part: "The programme will be between the national government and the County Government of Nairobi and will cost billions of shillings.
"It focuses on key economic and social sectors and is expected to significantly improve the livelihoods of Nairobi residents," it went on to state.
Nairobi County Assembly Minority Leader Peter Imwatok stated: "As the assembly, we want to know the law they followed and who will supervise this (Sh17 Billion) fund. Our priority is to ensure value for money."
10:05 AM : Governor Sonko posted on his Facebook page that the report was false and the authors of the report were attempting to blackmail him. He maintained that his relationships with the Deputy Governor and the National Government were good. He went on to post screenshots of conversations he regularly has with the Deputy Governor on the progress of various initiatives.