The dispute threatens to disrupt the power-sharing government, which was formed by the two rivals to end bloody clashes triggered by a presidential poll in which both men claimed victory.
'Accordance with the law'
In response to Kibaki's revoking of the suspensions, Odinga called on Kofi Annan, the former UN secretary-general and negotiator of the power-sharing deal in 2008, to intervene in the standoff.
"Legally and constitutionally, neither the president nor the prime minister is superior to the other"
deputy prime minister
"The national accord expressly stipulates that both principals agreed to share power equally in order to bring peace to this country," a statement read out by Musalia Mudavadi, the deputy prime minister, said.
"Legally and constitutionally, neither the president nor the prime minister is superior to the other. The prime minister acted strictly in accordance with the law."
Odinga said that two recent investigations, one into an alleged $26m subsidised maize scam and the other into the reported disappearance of $1.3m at the education ministry, had "laid credible foundations for the two ministers to be investigated".
Ruto is a member of Odinga's own group within the coalition while Ongeri is an ally of Kibaki.
Odinga's attempted move had followed similar actions against eight other officials by Kibaki.
Kibaki said on late on Saturday that he had suspended the officials 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.
Among the suspended officials were Mohammed Isahakia, the permanent secretary in Odinga's office, and Karol Omondi, the prime minister's chief of staff.
Tensions have risen since both Kibaki and Odinga allies were implicated in the scandals.
In January, the US, Kenya's largest single aid partner, suspended a $7m assistance programme at the education ministry "until there is a credible, independent audit and full accountability".
The infighting also sparked criticism by Nairobi's Western allies of the slow pace of implementing reforms to prevent a repeat of the violence that rocked Kenya in early 2008, killing about 1,500 people.
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.