Deputy Chief Justice Philomena Mwilu will not be prosecuted as the evidence by the DCI was obtained illegally, the High Court ruled on Friday.
Appearing before a 5-judge bench, DCJ Mwilu was facing alleged fraud and abuse of office charges.
"DCI's way of obtaining the evidence has irredeemably rocked the foundation in which the charges stand," the judges ruled.
The Judges; William Musyoki, Mumbi Ngugi, Hellen Omondi, Francis Tuiyott and Chacha Mwita also found that the abuse of office charge ought to have been handled by the JSC.
The Directorate of Public Prosecution (DPP) stated that they would appeal the decision.
Mwilu was represented by lawyers Nelson Havi and Senator James Orengo.
The judge had been under investigation for months after being reported by the Kenya Revenue Authority (KRA) to the DPP over the suspicious transfer of large amounts of money in and out of several bank accounts.
The top judicial official faces numerous counts of stealing, abuse of office and tax evasion.
Investigations also implicated the judge in the collapse of the imperial bank after accepting a personal loan of Ksh12 Million.