The International Criminal Court (ICC) has dropped charges against Francis Muthaura, a co-accused of Kenya's presidential election winner Uhuru Kenyatta.
Fatou Bensouda said some witnesses were too scared to testify, while another had recanted his statement.
Mr Muthaura was accused of fuelling violence after the 2007 election.
Lawyers for Mr Kenyatta, who won last week's elections, said similar charges against him should now be dropped.
His trial is due to start in July.
Mr Muthaura, a former civil service chief, was on the same side as Mr Kenyatta during the disputed 2007 election, after which more than 1,000 people were killed and about 600,000 were left homeless.
Mr Kenyatta is accused of organising attacks on members of ethnic groups seen as supporting Raila Odinga against President Mwai Kibaki. He denies the charges.
Mr Muthaura was accused of five counts of crimes against humanity, including authorizing the police to use excessive force against protestors during the violence that swept through Kenya after the 2007 election.
The BBC's Gabriel Gatehouse reports from the Kenyan capital, Nairobi, that the decision to drop charges against Mr Muthaura could have a bearing on the case against Mr Kenyatta, who beat Mr Odinga in the 4 March election.
Both men were accused of developing a plan to get the feared Mungiki sect to attack ethnic Kalenjins, seen as supporters of Mr Odinga in 2007.
But a key witness - known as witness number four - who had been due to testify that Mr Muthaura had been present at a meeting where this plan was formulated, has admitted lying and taking bribes and so his evidence has been dropped.
However, Ms Bensouda stressed that her decision had no bearing on Mr Kenyatta - and nor was it affected by the election result.
"Let me be absolutely clear on one point - this decision applies only to Mr Muthaura," she said in a statement. "It does not apply to any other case."
Ms Bensouda said she had dropped charges against Mr Muthaura because several people who may have provided important evidence had died, while others were "too afraid" to testify for the prosecution.
She also noted the "disappointing fact" that Kenya's government had failed to provide important evidence, and failed to facilitate access to witnesses.
"While we are all aware of political developments in Kenya, these have no influence, at all, on the decisions that I make," Ms Bensouda added.
Mr Kenyatta's lawyer Steven Kay called on Ms Bensouda to reconsider the case against him, AP news agency reports.
"In light of what the prosecution has said... they should consider their position honestly in relation to Mr Kenyatta,'' he is quoted as saying.
"The evidence they are seeking to rely on is utterly flawed."
Mr Muthaura was among six people who were originally charged by the ICC - two others, Hussein Ali and Henry Kosgey, had charges against them dropped earlier.
Mr Kenyatta contested the 4 March election, despite being charged. He said he was innocent and vowed to clear his name in court.
He won with 50.07% of the vote, compared with the 43.31% for Mr Odinga.
Mr Odinga is challenging the result in court, claiming it was marred by irregularities.
In 2007, he lost to Mr Kibaki, who is now stepping down at the end of his two terms.
Mr Kenyatta backed Mr Kibaki during the 2007 election.
His running mate in last week's election, William Ruto, supported Mr Odinga in 2007.
Mr Ruto is also due to stand trial at The Hague for orchestrating violence against supporters of Mr Kibaki in 2007 - he strongly denies the allegation.