EACC wants Waikenda charged alongside an assistant director Abraham Mwaura for abuse of office.
The EACC file recommending charges against the two was sent to the Director of Public Prosecutions Keriako Tobiko on Friday.
“EACC.FL/INQ/45/2014. Inquiry into allegations of irregular issue of permits by the Department of Immigrations. EACC recommends that the suspects be charged with abuse of office,” a statement from the commission indicated.
Waikenda was being investigated over the issuance of more than 300 work permits in October 2013.
EACC also wants administrative action taken against the former National Social Security Fund Managing Trustee Richard Langat for exposing the fund to contractual obligations when the funds needed to finance it were not available.
“The file was initially submitted to the DPP with a recommendation for administrative action against the suspect. The DPP ordered for further investigations. The file has been resubmitted and EACC found no criminal culpability on the part of any member of the board ort management of NSSF,” the Anti Corruption body said.
EACC has also recommended charges against former Chief Registrar of the Judiciary Gladys Boss Shollei over the irregular payment of Sh46 million for the construction of pre-fabricated courts in Mavoko.
The anti-graft body stated that Shollei will be charged alongside the Deputy Chief Registrar Kakai Kissinger, the director of supply chain Martin Otieno and the Finance Director Benedict Omollo.
Others facing charges in line with the irregularity include Judiciary Tender Committee members, Wycliffe Wanga, Nicholas Okemwa and Thomas Oloo.
The irregularity came up at a time when the Judiciary was involved in the construction and repair of court buildings countrywide.
The Director of Public Prosecutions said that all cases will be reviewed and decisions made based on evidence and law.