The outspoken Member of Parliament for Assin Central,
He said the decision by EOCO to storm the offices of the Deputy Commissioner of the Electoral Commissioner, Mrs Georgina Opoku Amankwah is a disgrace.
The deputy EC boss is being investigated along with two others over the missing of GH¢480,000.
Some Police personnel with AK 47 assault rifles led by the Acting Executive Director of the EOCO, ACP K.K Amoah (Rtd) stormed her office.
She had been on a forced leave since July 2017 at the instance of the investigative agency.
Her resumption in office was against an advice from the investigative body urging her follow due process since their investigations into the Staff Endowment Fund of the election management body has not been concluded.
Apart from Mrs Opoku Amankwah, two other EC officials also being investigated in connection with the GH¢480,000 are Finance Director Dr Joseph Kwaku Asamoah and Chief Accountant Kwaku Owusu Agyei-Larbi.
The money in question was allegedly withdrawn from the Endowment Fund of the EC between 2012 and 2013 by the three officials during the tenure of Dr Kwadwo Afari Gyan as EC Chair and used for official business pertaining to the commission.
But Kennedy Agyapong said he could not understand why Mrs Opoku Amankwah has been singled out when all the EC bosses under investigation are still in their offices.
"The principle by EOCO was wrong. EOCO is a bogus organization. They are very bias. I know there are officers who have been accused but why have they turned their guns on only one person. I don’t know that woman but I think they have not been fair to her," he said.
Speaking on Adom TV, the maverick politician accused some members of the ruling government at the Flagstaff House of protecting the EC boss, Charlotte Osei.
"NPP members are protecting and taking orders from EC boss; I don’t hate Charlotte Osei but her utterances and behavior is very bad and needs to be condemned. I know some small boys at the Flagstaff House are influencing the situation and are only embarrassing the President.
"I receive calls from some judges telling me that some small boys at the Flagstaff House are frustrating lawyers on the case and are making issues worse," Kennedy Agyapong said.