"We will not drop the charges," Fatou Bensouda told reporters in Paris, saying it was only a question of when, not if, he goes to trial.
Kenyatta (51) stands accused of orchestrating deadly violence that followed disputed polls five years ago. He was named Kenya's new president in a closely-fought election this month, though his main rival has filed a legal challenge against the win.
Bensouda said she deplored the lack of co-operation from the Kenyan government in the International Criminal Court cases related to the East African country, which she said suffered from witness intimidation.
"Kenya is the most challenging situation our office has had to deal with," she said.
Lawyers for Kenyatta on Monday urged the ICC to dismiss the case against him after prosecutors last week dramatically dropped all charges against Kenyatta's co-accused after a key witness withdrew testimony.
It was the first time ICC prosecutors decided to drop a case since the world's first permanent independent war crimes court began operating in 2002.
Should the charges against Kenyatta stand, he will become the first-ever president to have to fly off to The Hague to face a trial that could last at least two years shortly after taking office.
Kenyatta, one of Africa's richest and most powerful men, was declared the president just over a week ago following the first elections after the African country's post-poll unrest five years ago in which ICC prosecutors say some 1 100 people were killed.
Prosecutors suspect Kenyatta of having paid the Mungiki, a sect-like criminal gang notorious for beheading its victims, to lead reprisal attacks and defend the Kikuyu community when violence ripped through the country.
Kenyatta denies the allegations.
His trial is scheduled to begin in July and he has repeatedly vowed to co-operate with the legal proceedings.
The evidence against Kenyatta's co-accused, top civil servant Francis Muthaura, was critically undermined when a key prosecution witness, known as "OTP-4", recanted earlier testimony.
Lawyer Steven Kay on Monday said the five charges against Kenyatta, including rape and murder, should now also be reconsidered.
Because of the withdrawal of that witness "this matter has to go back for reconfirmation by the pre-trial chamber", Kay told the court, saying this witness' statement "is the backbone of the prosecution's case from the beginning to end".
"To a certain extent we have lost faith in the decision-making as we warned the pre-trial chamber of the quality of the evidence and we were ignored," Kay said.
More than 663 000 people were displaced in Kenya's Rift Valley five years ago after fights between rival supporters, prosecutors said, when politically motivated riots soon turned into ethnic killings, which in turn sparked further reprisals.
The clashes destroyed Kenya's image as a beacon of stability in the region, hurt its tourism industry and exposed long-simmering ethnic rifts among its population. – Sapa-AFP