The Nyeri government paid all its staff Sh30 million leave allowance for two months despite the lack of approval forms.
Auditor General Edward Ouko has revealed that the Sh30,068,506 was paid in December 2014 and February 2015.
"Further, the possibility of all officers proceeding for annual leave concurrently in one month is untenable," Ouko says in a report released on Monday.
"The payment was therefore unjustified and was paid contrary to the code of regulations."
He added that the accuracy of the compensation could not be ascertained as the audit revealed an unjournalised expenditure of Sh491.8 million.
This is one of the queries that led Ouko to conclude that the county may have misused 47 per cent of its total funds in the 2014-15 financial year.
The county government provided the Auditor General with an expenditure of Sh2.3 billion in the 2014-15 financial year that was unsupported by relevant schedules and ledger.
Ouko reports that due to the significance of the unsupported amount, his office was unable to state whether 47 per cent of the total county funding was used effectively and in a lawful manner.
The report further shows that Governor Nderitu Gachagua's office paid Sh15.8 million to the Kenya Red Cross Society before emergency services were rendered.
It also revealed that Deputy Governor Samuel Githaiga got an owner-occupier house allowance of Sh2.5 million yet he does not qualify for a house benefit under the law.
The audit also revealed that there was an imprest balance of Sh9.2 million yet the statement of assets provided by the county government listed a figure of Sh5.8 million.
The report also says the county did not disclose how much it had received from rent and rates thereby failing to comply with laws on county government financial reporting.
As has been noted in many counties, the Nyeri Treasury did not post the Sh4.1 billion received from the exchequer or any other money amounting to Sh8.89 billion from funds singly generated and transfers from other government entities.
The audit shows that while the county's financial statements show it paid Sh4.9 billion during that financial year, the IFMIS record shows that the amount was Sh4.3 billion.
The county government also did not collect revenue worth Sh704 million (51 per cent) from various sources and did not give auditors an explanation.
The report also says Nyeri did not explain where it got an extra Sh18.5 million to fund six projects that were to cost Sh29.1 million.
It also shows that Nyeri Provincial General Hospital and Karatina hospital got unapproved waived fees of Sh20.5 million and Sh14.1 million respectively.
The report also shows Nyeri County Referral Hospital awarded a Sh27.4 million tender for installation of 10 dialysis machines and a water treatment system, and the supply of 1,000 complete dialysis kits.
But a physical inspection carried out on September 28, 2015 showed four of the 10 dialysis machines had malfunctioned while the kits worth Sh3.8 million id not fit into them.
The county government procured medical equipment worth Sh25.6 million during that period but the physical inspection found the equipment had never been used.
For all county audit stories visit the Devolved Corruption section