Kirinyaga Governor Anne Waiguru wants the Integrated Financial Management System (Ifmis) director to explain how 11 counties ended up with more than Sh10 billion in bizarre expenditures.
"There is nothing wrong with the system. A system is as good as its people. A system does not just generate reports," Governor Waiguru said.
Ifmis has five modules: procurement, cash management, accounts receivable, budget and the general ledger.
Ms Waiguru said trouble started when counties logged into the system and found two reports. One was the correct one and the other had an underscore.
Those who clicked on the erroneous one ended up with wrong reports, the Kirinyaga County boss told the Nation. "Just who designed the reports that linked county governments to the national government budget?" she asked.
Kakamega Governor Wycliffe Oparanya wants the Directorate of Criminal Investigations to investigate the issue.
"Governors read mischief in this saga that has raised queries on the safety of Ifmis, which was supposed to bring transparency in financial management," Mr Oparanya said.
Governors also worry that their budgets may have been used by fraudsters at the Treasury to hide stolen billions of shillings and balance their accounts.
In the reports generated by the Auditor-General, Samburu, for example, had an allocation to the East Africa Customs Union while Kitui and Kakamega counties reportedly spent Sh60.56 million and Sh29.3 million respectively on State House functions.
Governor Ferdinand Waititu's Kiambu was said to have allocated Sh793 million to free primary education, a national government expenditure.
What is more, Mr Waititu also "splashed" Sh180 million on ex-Presidents Mwai Kibaki and Daniel Moi.
His administration had another Sh58 million to spare to support the peacekeeping mission in troubled South Sudan.