Kenya is battling a wave of extremist attacks by al-Qaida-linked al-Shabab militants from Somalia that has killed more than 400 people since October 2011 when the country sent troops into Somalia to fight the militants.
Al-Shabab has vowed to avenge the Kenyan military presence.
Kenya has been working closely with American security agencies in the fight against extremism and the meeting with Obama will further strengthen this cooperation, Kenyatta said.
Deputy President William Ruto and radio station head Joshua Sang are on trial for allegedly orchestrating the violence following a disputed presidential election in late 2007. More than 1,000 people died and 600,000 people were displaced from their homes
The International Criminal Court dropped similar charges against Kenyatta in December, citing a lack of sufficient evidence for the decision, which it attributed to witness intimidation and lack of Kenyan government cooperation.
"The deputy president is part of this government so we shall all be meeting and proceeding with what we need to do," he said. "All I can say is that those who doubted the strength of the friendship between the two countries, or the depth of our engagement, had better re-examine their assumptions." Obama's father is from Kenya.
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