Kenya has set up a commission of inquiry to investigate a serious breach of security at Nairobi's main airport.
Mr Kibaki is trying to distance himself from the affair
Earlier police Criminal Investigations Department (CID) head Joseph Kamau and 11 other officials were suspended.
The incident involved two Armenian brothers who brandished weapons when challenged to open their luggage by airport security staff last week.
Instead of being charged, they were quietly deported, prompting claims they were receiving top-level protection.
The two Armenians first came to public attention during a controversial raid on a Kenyan newspaper in March.
On Sunday, President Mwai Kibaki denied newspaper reports of a family connection with the men.
The pair, Artur Sargasyan and Artur Margaryan, have always maintained that they are innocent businessmen.
Cache of weapons
The BBC's Karen Allen in Nairobi says Mr Kamau's suspension is the latest in a bizarre story of political intrigue which the president has tried to distance himself from.
The Armenians known as the Artur brothers had aroused suspicions since March when masked armed men raided the Standard newspaper in Nairobi.
Ministers said the operation was carried out on security grounds, but questions arose when it became clear that Kenya's most senior police officer had not been informed about the target of such a sensitive operation.
Since then, a cache of weapons, balaclavas and body armour has been found at the Artur brothers' Nairobi home, similar to those used in the raid.
Government-issued car number plates were also found.
But no charges have been brought so far.
Diplomats have been putting pressure on the Kenyan government to explain who these men are amid concerns that the Armenian brothers have been allowed operate with protection from top levels of government.