At least 44 county governments can now access their share of revenue from the national government following the Senate's arrival at a consensus last week.
Controller of Budget Margaret Nyakang'o said counties are to get Sh60 billion and that 44 of them have submitted relevant documents and uploaded budgets onto the Integrated Financial Management Information System (Ifmis).
"Everything is in order. They are just waiting for the money to be credited into their accounts. Unfortunately, three counties are yet to submit their documents for uploading to the system so they can be allowed to access their cash," Dr Nyakang'o said in an interview.
The three are Mandera, Wajir and Kitui, whose assemblies were yet to approve their budgets by Monday. In Wajir, a stalemate between the executive and the assembly delayed the budget process.
Ms Nyarang'o said she will get in touch with the three in an effort to fast-track their budget processes so they can get the much-needed money.
"The three counties can view the County Revenue Fund but they cannot access it," she said.
They can use locally sourced revenue to finance their operations in the meantime.
Ms Nyarang'o further said Senators will Tuesday pass the County Allocation of Revenue Bill, 2020, which will be taken to the National Assembly and thereafter to President Uhuru Kenyatta for assent to provide the basis for sharing funds among counties.
The government's move came about a week after Senators reached a consensus on disbursing Sh316.5 billion to counties, ending a revenue standoff that lasted about three months and threatened to cripple operations.
On September 18, Treasury Cabinet Secretary Ukur Yatani said the devolved units will receive Sh60 billion this week following the consensus on the third basis formula for revenue allocation.
CS Yatani said this is part of the Sh316.5 billion revenue for the 2020-2021 financial year. The money remained in the Treasury as the stalemate over the revenue-sharing formula raged on.
The law does not allow the Treasury to disburse money from the Consolidated Fund without the authority of the Senate and the National Assembly.
Cash from the Consolidated Fund cannot be disbursed in the absence of a written law on either appropriation or a direct charge.
The Senate had failed a record 10 times to unlock the deadlock despite numerous consultations and several weeks of negotiations, in what exposed deep political divisions.
The stalemate stalled passage of the County Allocation of Revenue Bill, which must be approved and signed into law by the President before counties get their money.
The standoff degenerated and caused divisions in political parties with members taking opposing stands.
The breakthrough came a day after President Uhuru Kenyatta pledged an additional Sh50 billion allocation to counties to supplement the Sh 316 billion.
In the formula approved last week, no county will lose revenue. Nairobi, Nakuru, Kiambu and Turkana will get the lion's share of the billions allocated to counties.
Nairobi, for instance, will get an additional Sh3.3 billion from the Exchequer, which will push its total allocation to Sh19.2 billion from the current Sh15.9 billion.
Nakuru's allocation will shoot to Sh13 billion from Sh10.4 billion while Kiambu will get Sh11.7 billion after an additional Sh2.2 billion and Turkana Sh12.6 billion, up from Sh10.5 billion.
Kakamega will get an additional Sh1.9 billion, Bungoma Sh1.7 billion, Uasin Gishu Sh1.7 billion, Nandi Sh1.6 billion, Kitui Sh1.5 billion and Kajiado Sh1.5 billion.