Ngilari was found guilty of not following due process in the purchase of 25 vehicles at the cost of N169 million.
In a statement on Friday, spokesman of the commission, Mr Wilson Uwujaren, described the ruling as “a travesty of justice’’.
An Adamawa High Court in Yola had on March 6 sentenced Ngilari to five years imprisonment after he was convicted of a five-count charge of corruption.
He was found guilty of not following due process in the purchase of 25 vehicles at the cost of N169 million.
But, the conviction was overturned by the Yola division of the appellate court on the ground that the charges against the former governor lacked merit and sufficient proof.
It would be recalled that Ngilari secured a suspicious bail after his conviction on the basis of a letter that cited his poor health condition.
The EFCC spokesman said the emergence of the letter was shrouded in suspicion and controversy as the Controller of the Nigeria Prison Service, Adamawa Command, reportedly expressed ignorance of the letter.
This subsequently incurred the wrath of the authorities at the prison, which issued query to officials involved, according to Uwujaren.
He said, “Pundits consider the decision of the Appellate Court, which was read by Justice Folashade Omoleye, as shocking, and the last thing needed by the current war against corruption being spearheaded President Muhammadu Buhari.
“It is curious that Justice Omoleye, while delivering the ruling, alluded to the fact that Ngilari was not ‘a procurement entity’ and as such, a former governor could not be charged ‘as if he was an ordinary procurement officer’.
“The commission has therefore resolved to appeal the ruling because the EFCC believes that the judgment is a travesty of justice”.