The health department and the executive were the biggest beneficiaries in a bill adopted by the assembly yesterday.
The bill detailed how Governor Hassan Joho's administration will spend Sh9.99 billion in the remaining part of the financial year ending June 30.
The allocations were contained in the Supplementary Appropriation Bill which is awaiting Mr Joho's signature.
Other major beneficiaries were the transport and water departments, and the county assembly.
The departments allocated the lowest amounts included tourism, agriculture and youth.
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Health services got Sh2 billion for recurrent expenditure and another Sh472 from appropriation in aid (that is money raised from local revenue). Recurrent expenditure includes salaries, wages and such expenses.
Sh370 million went to development expenditure with an additional Sh122 million expected to be raised as appropriation in aid.
Salaries and other expenses at the county executive's headquarters are to gobble Sh836 million, with an additional Sh401 million coming from appropriation in aid.
The county assembly was allocated Sh675 million for recurrent expenditure, with a further Sh324 million from appropriation in aid.
For development, the county assembly allocated Sh63 million.
The department of water was allocated Sh530 million plus another Sh254 million for recurrent expenditure.
Port Reitz MCA Fadhil Makarani moved the motion that sailed through without any opposition from the assembly.
He represented Finance Committee Chairperson Mohamed Hatimy who was not in the assembly.
"Passage of this bill is significant to the residents of this county because it will enable the county government settle water bills and end frequent disconnection of supply that recently resulted in a crisis," Mr Makarani said.
Three weeks ago, the Coast Water Services Board disconnected water supply to the county over a Sh608 million bill accrued since July 2013.
The supply was restored after the county, through the Mombasa Water and Sanitation company, paid the bill.
In total, the county government seeks to spend Sh6 billion on recurrent expenditure and Sh3 billion on development.
Mtongwe Ward Representative Hamisi Mwidani urged members to endorse the bill to enable the government purchase the Mtongwe ferry as factored in the current budget estimates.
"I am happy that this bill has been presented before the assembly. We should all support this legislation so as to enable the government to purchase a new ferry to service the Mtongwe channel," Mr Mwidani said.