The decision on Thursday means the trial should go ahead as planned on February 5 and will likely further strain relations between the Hague-based International Criminal Court and the country.
Kenyatta and his deputy William Ruto face separate charges of stoking ethnic violence after the country's 2007 elections, when 1,200 people died. The cases have become a rallying point for the ICC's critics, including many other Africa leaders, who accuse it of singling the continent out for prosecution.
Since Kenyatta was elected in the spring, Kenya and its African Union allies have sought to have his trial shelved, saying it risks destabilising a country that is essential to the security of the entire east African region.
Judges said they were "concerned" by evidence presented by Kenyatta's lawyers suggesting that individuals had been paid to coach witnesses against Kenyatta and that others had colluded to give false testimony for financial gain.
But they said Kenyatta's defence team could challenge any false testimony in court, making it unnecessary to halt the trial.
In November, Kenyatta's supporters notched up a diplomatic victory when they persuaded the court's member states to adopt a change to the court's rules allowing heads of state to skip trial in order to attend to their constitutional duties.
But that rule-change, which has yet to be tested in court, could be challenged by prosecutors and by lawyers for the victims of the violence that swept Kenya in late 2007 and early 2008.