In a letter reportedly sent by deputy secretary general Pere Miró, the IOC also offered to host both bodies at its headquarters in Lausanne for a meeting in an attempt to resolve the dispute.
Kenyan Sports Minister Hassan Wario disbanded the National Olympic Committee of Kenya (NOCK) on August 25, citing a catalogue of logistical and mismanagement issues which "damaged the morale of athletes" during Rio 2016.
NOCK secretary general Francis Paul and vice-chairman Pius Ochieng were among those arrested before being granted bail last week.
"We sincerely hope that the present situation will be rectified without delay, failing which the IOC would, unfortunately, be forced to consider protective measures vis-à-vis your NOC and the Olympic Movement in your country, as provided in these circumstances in the Olympic Charter, in particular Rule 27.9," the International Sports Press Association (AIPS) and other Kenyan media report that Miró wrote in his letter, addressed to NOCK chairman Kipchoge Keino.
"In view of the above and as a first step, we urge the Government authorities of Kenya to take immediate action to rectify the situation and fully respect the jurisdiction of your NOC, as recognised by the IOC, in order for your NOC to resume its work and activities with full access to its properties.
"We also encourage the Government authorities and your NOC to engage in a serene and constructive dialogue, with mutual respect, to clarify any misunderstanding which might have led to this regrettable situation, and establish fruitful cooperation for the future, which is no doubt necessary for the development of sport and the athletes in your country.
"If necessary, we would be ready to organise a joint meeting with your NOC and the relevant Government authorities at the IOC headquarters in Lausanne."
Rule 27.9 of the Olympic Charter provides the IOC's ruling Executive Board to "take any appropriate decisions for the protection of the Olympic Movement in the country of an NOC, including suspension of or withdrawal of recognition".
The NOCK would have "an opportunity to be heard" before any such decision is taken, with no further meetings of the Executive Board scheduled until December.
The organisation are accused of key accommodation and travel mishaps, including the "mishandling of accreditation", as well as kits which never reached athletes.
Other problems at Rio 2016 included a doping scandal in which a coach was expelled from the Games for impersonating an athlete, selection issues and tension between Athletics Kenya and the NOC.
Keino, awarded the Olympic Laurel during the Opening Ceremony of Rio 2016, is the only senior NOCK figure who has yet to be charged.
But the Mexico City 1968 1500 metres and 1972 3,000m steeplechase champion and IOC honorary member told Citizen Digital that he was questioned for five hours by Government officials last week in Eldoret.
The disbanding marked another breakdown in relations between an NOC and a National Government, something the IOC had sought to avoid by tightening its rules on autonomy and Government interference.
Patrick Hickey was appointed as the IOC autonomy delegate in 2014, but remains under house arrest in Rio as investigations continue both in Brazil and in Ireland over his alleged involvement in an alleged ticketing scandal surrounding the Olympic Council of Ireland.
Kuwaiti athletes competed independently at Rio 2016 after their NOC was suspended last year for such Government interference.