The witness, who does not wish to be named for security reasons, has written ICC Chief Prosecutor Fatou Bensouda informing her of his decision to withdraw his evidence against Ruto.
In an affidavit sworn on May 9 2013, the witness from Uasin Gichu County, said he no longer wishes to testify in the Hague. "You have listed me as one of the witnesses against the accused person in Case No 1. I have now reconsidered my position in this case and I no longer wish to testify against any of the accused persons," he said in his letter.
"I do not therefore intend to be present and or testify before the court in support of your case," said the letter sent through lawyer Paul Gatonye.
He said his decision was voluntary without any influence from anybody. In his sworn statement, he said that he was a PNU official during the 2007 general election and that he was induced to testify against Ruto.
He was relocated to Tanzania together with his family and promised to be settled abroad if he testified before the ICC. The withdrawal comes just two months after another ICC witness refused to testify against Ruto.
In March, the first witness recanted allegations implicating Ruto, radio presenter Joshua Sang and former minister Henry Kosgey (who has since been cleared).
The first witness, who initially claimed that Ruto helped to plan and finance 2007-2008 post election violence in Rift Valley, asked Bensouda to withdraw "each and very piece of evidence attributed" to him.
He claimed that he was coached by Kenyan human rights activists and ICC officials to give false accounts of the violence in which 1,300 people died and 350,000 were displaced.
The case against Ruto was to start on May 28 but was postponed this week by the Trial Chamber. A status conference on May 14 will set a new date.
Meanwhile, Bensouda told the UN Security Council on Wednesday that Kenya was making a "backdoor attempt to politicise the judicial processes" of the ICC.
Bensouda said that Kenya was making "unfounded and incorrect" claims while urging the UN to terminate the cases facing President Uhuru Kenyatta and Ruto.
Bensouda said that she has not received a copy of the letter sent to the Security Council by Macharia Kamau, Kenya's ambassador to the UN. She said that she reserved the right to respond in detail once the document is released officially.
On Thursday, Ruto's lawyer Karim Khan told the media that his client was unaware of Macharia's letter and it had not been officially authorised by government.
The lawyers for Ruto and his co-accused, broadcaster Joshua Sang, said that they have confidence in the ICC and that they will eventually be found innocent.
It is believed that Ruto's statement distancing the government from the letter had the blessings of the President who is also said to have been "unhappy" with the letter.
"The ICC has always and will always continue to respect the sovereign equality of all states. The ICC will not shy away from investigating individuals for any alleged crimes irrespective of their status," Bensouda told the Council.
The Prosecutor was responding to earlier comments made by Rwandan ambassador, Eugene-Richard Gasana, who said that Macharia's letter makes "a compelling case against the methods of work of the office of the prosecutor on the Kenyan cases".
Gasana claimed that the ICC had been "selective in its methods of investigating and prosecuting perpetrators of serious international crimes as it has failed to prosecute similar crimes committed in other parts of the world with impunity". The Security Council session was discussing crimes committed in Libya during the pro-democracy uprising in 2011.