County governments operations could grind to halt following the collapse of the Integrated Financial Management Information System (IFMIS) last month.
Already, some counties which had no money to pay December salaries have been forced to borrow from the banks.
According to the Council of Governors (CoG), the failure of the system has adversely affected counties' activities.
The council's Finance Committee chairman, Governor Wycliffe Oparanya (Kakamega) is, however, alleging a ploy by the Government to frustrate counties and portray them as lacking the capacity to handle the devolved functions.
"IFMIS is not working up to now. In the case of Kakamega, I have managed to pay staff some money after negotiating for a loan from Co-operative Bank," said Mr Oparanya, when contacted on phone by The Standard.
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He added: "It is one of the schemes to frustrate county governments. How comes the Government, which is the biggest spender, can allow a system such as IFMIS to collapse without thinking of alternatives? We have tried to reach the National Treasury Cabinet Secretary Henry Rotich to discuss the matter but he is not available."
But in response, Mr Rotich said all the issues pertaining to the IFMIS were addressed before Christmas.
"Indeed, teachers received salaries on December 23. You can confirm with Teachers Service Commission (TSC). IFMIS is working and if they have not been paid then it is something else," he said.
Oparanya warned that if counties fail to pay their staff the December salaries, it will be a big blow to them and the impact will be felt in their work output.
"This could lead to paralysis of county operations. The governors will be discussing this issue tomorrow (today) with a view of escalating the matter with Treasury. This is not the first time counties are raising concerns over the functionality of IFMIS," he stated.
Bungoma Governor Ken Lusaka, who also the media liaison coordinator of the council, also raised concern over the failure of the system, now forcing counties to borrow from banks.
But even as the governor raised the red flag, thousands of the employees of the Nairobi County Government can now breath a sigh of relief as their December salaries is out.
