NAIROBI -- Kenya's Olympic body top official Francis Kanyili Paul has stepped down over graft cases linking him to the 2016 Rio Olympics.

Kanyili, secretary-general of the National Olympic Committee of Kenya (NOCK), together with others has been indicted for his role in overseeing the 550,000 Rio Olympic Games scandal. His assistant Francis Mutuku has since replaced him.

NOCK president Paul Tergat confirmed on Wednesday the new development promising to respond in transparent manner on any issues the courts and investigators will seek from the IOC affiliate body.

Despite Kenya registering one of its best show in Olympic Games history, winning six gold, six silver and one bronze medals, all from athletics, the country subjected its athletes to worst preparations condition in the build up to the games.

"Francis K. Paul has opted to step aside to allow for the completion of his corruption case at the High Court. His deputy Francis Mutuku will step in," said Tergat on Wednesday.

Tergat warned that the country will not afford to rest on its laurels ahead of next year which will see several sports disciplines compete in Olympic qualification tournament.

"We have the Africa Games in Morocco due next year, some federations will have regional qualifications hence more funding will be required. A few federations have given us their tentative requirements for next year," said Tergat.

The Olympic body has been doing a forensic audit, and Tergat said they will have a retreat in Nyeri to discuss it besides other governance issue.

"A final report on the audit will be made public in the next few weeks. Importantly will be the recommendations from the report," said Tergat who was selected into office in May.

"Since I took over NOCK, it has been a turbulent tenure with ghosts of the previous regime tormenting us. It has never been easy, with the restructure process we have undertaken so as we may encourage sponsors to come back and improve our relationships with the government," said Tergat.

The local International Olympic Committee (IOC) body besides its debts from engaging in sports administrations is also building its headquarters in Nairobi and has run late in payment of premiums to its contractors and bank loans estimated at 800 million shillings (about $8 million).