Speaking during a joint parliamentary group meeting bringing together members of the United Democratic Alliance and the Orange Democratic Movement, the president dismissed the reports as misleading and politically driven.
Ruto argued that the figures cited in the report do not reflect the actual situation within the national health financing system.
According to him, if such a large amount had truly disappeared from the fund, hospitals across the country would already be facing severe payment challenges.
Instead, he maintained that the system continues to operate normally and healthcare facilities are receiving funds for services offered to patients.
The president said the government has recently made significant payments to health facilities under the Social Health Insurance Fund.
He revealed that within the current week alone, hospitals received a combined Ksh16.2 billion for services delivered under the insurance programme as well as primary healthcare support.
Ruto insisted that the current administration is disbursing more funds to medical facilities than any previous government.
While defending the government’s handling of the programme, the president also linked the reforms to the broader plan of expanding universal health coverage in Kenya.
He explained that the administration is investing heavily in health services to ensure that ordinary citizens spend less money when seeking treatment.
According to him, the government is addressing several major areas that influence the cost of living including healthcare, education, fuel prices, and food supply.
The controversy follows an audit report by Auditor General Nancy Gathungu which raised concerns about irregular claims made through the Social Health Insurance Fund managed by the Social Health Authority.
The audit reviewed transactions recorded between July 2024 and June 2025 and highlighted several cases where medical claims appeared unrealistic or exceeded expected limits.
Among the most striking findings were claims showing the same patient undergoing open heart surgery four times in a single day.
The audit indicated that such cases were recorded thousands of times, resulting in payments amounting to hundreds of millions of shillings.
In another example, some records suggested that the same mother delivered a child up to ten times within one year, an occurrence that raised serious questions about the accuracy of the claims.
Health Cabinet Secretary Aden Duale had earlier acknowledged attempts to defraud the health insurance system but insisted that strict digital verification tools have helped stop many of the suspicious payments.
According to Duale, the verification platform identifies unusual medical claims before they are approved, allowing authorities to reject fraudulent submissions.
Government figures show that by February 2026, about 29.7 million Kenyans had already registered under the new health insurance programme.
During the same period, the Social Health Authority collected Ksh142.78 billion in contributions and paid out about Ksh105 billion to healthcare providers across the country.
Officials say these figures demonstrate that the programme remains financially active despite the concerns raised in the audit report.