Kibaki said on late Saturday he had suspended the eight officials, also for three months, after they were "mentioned adversely" in reports on the work of the subsidised maize scheme and Kenya's free primary education programme.
A statement from Kibaki's office said: "President Kibaki once again reaffirmed the government's commitment to fighting corruption and assured of speedy and conclusive investigations on use of public resources."
Among the suspended officials were Mohammed Isahakia, the permanent secretary in Odinga's office, and Karol Omondi, the prime minister's chief of staff.
International donors and the Kenyan public have long called on the government to take tough action against influential individuals blamed for a series of corruption cases that have tainted several important sectors of east Africa's biggest economy.
Donors will welcome the action against senior figures, who include officials from the National Cereals and Produce Board and the permanent secretaries in the ministries of agriculture, education, special programmes and prime minister's office.
But many Kenyans said the move by Kibaki highlighted growing rifts between the president and Odinga, the opposition leader who became prime minister after talks to end post-election violence in 2008 that killed at least 1,300 people.
Tensions have risen since Kibaki allies were implicated in the education scandal before senior Odinga allies were implicated in the bigger maize procurement case.
The issue of how to deal with high level corruption has soured relations in recent weeks.
The United States and Britain have both banned a number of Kenyans from travelling to their countries because of graft.
Last month, a US diplomat warned that Kenya risked another eruption of violence even before its next presidential poll in 2012 if reforms were not put in place soon.