Kenya’s digital payment system, eCitizen, is at the center of a heated political and financial storm. Billions of shillings are in question, and Kenyans are demanding answers. The Auditor General, Nancy Gathungu, recently released a report claiming that more than Ksh9.6 billion had gone missing from the platform.
However, Treasury Principal Secretary (PS) Chris Kiptoo is pushing back hard. Appearing before the National Assembly’s Public Accounts Committee on Thursday, August 7, he called the report misleading and insisted that not a single shilling had been lost.
“I want to assure Kenyans that from 2023 onwards, no money has been lost, to my knowledge,” Kiptoo stated firmly. His words were meant to calm public fears, but they also set the stage for a tense standoff between the Treasury and the Auditor General’s office.
The report in question was part of a special audit released in March 2025. It looked into the platform’s operations for the financial year ending June 30, 2024. The Auditor General highlighted over Ksh9.6 billion in questionable transactions, citing poor oversight between government ministries, departments, agencies, and financial service providers.
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Kiptoo said the claims were based on “an inaccurate distortion of the facts.” According to him, the government had already put strong measures in place to protect public money. He explained that after a formal contract was signed with the eCitizen system’s vendor, all previous loopholes for corruption were sealed.
“For almost 10 years, there were no contractual obligations between the vendor and the government,” he admitted. “We have now regularised the law and tightened the accounting systems to prevent misuse of funds.”
One issue that Kiptoo acknowledged was a mistake in how service charges were applied. The Auditor General had flagged the government for failing to implement a prorated service charge. Instead, a flat Ksh50 convenience fee was charged to users, which led to an overcollection of Ksh1.8 billion from taxpayers. While this overcollection is significant, Kiptoo stressed that it was not theft—rather, it was a policy oversight.
Another key point of dispute is ownership of the eCitizen platform. Some critics have suggested that the system might be partially controlled by outsiders. Kiptoo dismissed those claims, saying that the government fully owns eCitizen. “The passwords and administrative rights for eCitizen are managed by the Directorate of Citizen Services under the Ministry of Interior,” he clarified.
Despite the controversy, Kiptoo praised eCitizen as one of Kenya’s most transparent revenue collection systems. He pointed out that the platform allows money to be traced more easily than in many other parts of government.
But Kiptoo also accused Auditor General Gathungu of not following proper procedure before releasing her report. He claimed that the National Treasury was never given the chance to review or respond to the findings before they were tabled in Parliament. “This is the disadvantage of a special audit,” he said. “We could have provided important clarifications.”
The clash between the Treasury and the Auditor General has left Kenyans wondering who is telling the full truth. For now, the PS maintains that the system is clean and that the reported billions are not missing. The Auditor General, however, stands by her report, creating a political and financial tug-of-war that is unlikely to end soon.
At the heart of the matter is trust: trust in government, trust in digital systems, and trust in public financial management.
eCitizen was designed to make payments easier and more transparent, but this dispute risks shaking public confidence. Whether this is a story of billions lost or simply billions misunderstood, one thing is clear: the eCitizen saga is far from over.
