National Health Insurance Fund (NHIF) Managing Director Geoffrey Mwangi was on Friday arrested by detectives from the Directorate of Criminal Investigations (DCI).
The arrest was reportedly over alleged obstruction of justice in an ongoing corruption probe.
Also arrested by detectives was Head of Finance Wilbert Kurgat.
The two were summoned to DCI headquarters along Kiambu Road and apprehended soon after they arrived.
They are accused of using their positions to try to block investigations into claims of graft at the insurance body.
The news comes as Kenyans question plans to raise NHIF contributions to support the Universal Health Coverage (UHC) pillar of President Uhuru Kenyatta's Big 4 Agenda.
After reports emerged indicating that salaried Kenyans would be forced to contribute 2 percent of their income, Health Cabinet Secretary Sicily Kariuki came out to clarify that such a decision had not yet been made.
"The government does not intend to raise NHIF monthly deductions for workers to 2 per cent. When the time comes for any increase, public participation shall be done.
"All the workers will be involved should there be such a plan, but that is not intended now as had been reported by some of the media houses," she stated.
Currently, employees contribute a mandatory monthly premium of up to 1,700 shillings while voluntary self-employees pay 500 shillings per month.
With 6.5 million beneficiaries enrolled at the moment, the government plans to double the number within the next four years.
