Rotich said there was a choreographed campaign to have him charged, and that leaders from both sides of the political divide used the matter during public rallies to achieve their goals.
Rotich questioned advice given to Uhuru to allow 28 people be charged. He was acquitted last week of 19 charges, which included conspiracy to defraud government, and violation of the Public Finance Management Act.
He said he was relieved that the burden he was carrying had been lifted off his shoulders. Rotich said it was awkward to be charged for offenses he had not committed.
"It was not a good experience for anyone to go through. It puts your life at a standstill. I have been waiting for all this time for the matter to end. My parents and children were deeply concerned since they have known me to be a man of integrity," said Rotich.
He said that "it was clear that games were being played by the Directorate of Public Prosecutions (DPP) since it was fishing for evidence".
The DPP, he said, withdrew charges against some accused persons and turned them to State witnesses after their arraignment.
Rotich said that it was interesting to be told that he had conspired with people that he had not met to defraud government.
"Majority of the witnesses were from Kerio Valley Development Authority. I do not know them. Those at the Treasury we worked together before they were turned against me. If the President that I worked under was advised by the people who were charging me and he felt that was okay, well and good."
Rotich maintained that no money was lost in the Arror and Kimwarer dams' deal. He said the media often quoted Sh63 billion, which he did not know the source.
He said he wondered where the alleged proceeds of the stolen cash might be because he did not have any foreign accounts.
Rotich noted that all his accounts were in local banks and that if he was involved in embezzlement of government funds, it would be seen through suspicious transactions.
"I have worked at the National Treasury, and I know the issue of illegal proceeds . You cannot charge anyone without corresponding stolen proceeds. Any stolen money should have corresponding assets that have been put in place. Why did the prosecution not say it had found the stolen money?" he said.
Rotich said that the government can now go on with the two projects since a feasibility study was done in the 1990s.
"On how much was lost in the deal, I want to tell Kenyans, you cannot lose Sh63 billion. Anyone telling you about that kind of money is not saying the truth since it was the total cost of the project. It cannot be that the entire amount had been expended. What was expended was the advance Sh7.7 billion," he said.
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Rotich said he believed that President William Ruto was on the right track to turn around the economy "since the measures he has put in place at the moment might not be unpopular but in the long run Kenyans will come to appreciate."
He was non-committal about his future plans, saying that he was happy to finally be a free man.