The Controller of Budget wants 43 counties probed for accumulating Sh35 billion debt.
Agnes Odhiambo in the 2016/17 implementation annual report recommended that the pending bills should be audited by the Auditor General to ascertain their validity.
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Ms Odhiambo identified pending bills as one of the key challenges county governments are grappling with that is hindering the effective implementation of budgets.
According to the report, counties owed Sh35 billion in pending bills at the end of the financial year.
“The pending bills consisted of Sh11.56 billion for recurrent expenditure and Sh24.29 billion for development expenditure respectively,” the report stated.
Three counties; Machakos, Mandera and Nairobi City had not submitted the status of pending bills at the time of finalising the report.
“Counties that reported the highest amount of pending bills were; Mombasa (Sh3 billion), Turkana (Sh2.9 billion) and Nakuru (Sh2.8 billion).
Kitui County reported nil pending bills as at June 30, 2017,” Ms Odhiambo noted.
In central Kenya, Muranga County accumulated Sh1 bilion in debts and pending bills while Kiambu is at Sh920 million.
Embu, Meru and Kirinyaga counties owe Sh860 million, Sh 832 million and Sh219 million in pending bills respectively.
Nyeri has Sh712 million in pending bills out of which Sh128 million is for recurrent expenditure while Sh584 million is owed for development projects.
Revenue collection in county governments took a 7.1 per cent dip in the financial year 2016/17.
The 47 counties raised Sh32.52 billion which was 56.4 per cent of the annual local revenue target of Sh57.66 billion.
Ms Odhiambo noted that Sh32 billion was a decline from the Sh35 billion generated in financial year 2015/16.
According to the report, Marsabit and Turkana counties surpassed their targets at 107.3 per cent and 103 per cent respectively, while Kisii at 37 per cent, Wajir at 33 per cent, Garissa at 23 per cent, and Mandera at 21 per cent recorded the lowest performance.
Nyeri County had targeted to collect Sh1 billion in local revenue, however, it raised Sh643 million.
Kiambu County planned to raise Sh3 billion but managed to collect Sh2 billion which was 66 per cent of the revenue target. Muranga met half of the planned target of Sh993 million to raise Sh506 million
Kirinyaga’s target was Sh743 million but collected Sh320 million.
Meru County achieved the highest collection against its targeted revenue collecting Sh552 million against a target of Sh773 million.
Tharaka Nithi collected the least in the region as it had targeted Sh200 million but only raised Sh78 million.