Justice E. A. Obile upheld the preliminary objection by the EFCC in the matter and struck out the matter on the grounds that it could not sit on appeal over an order made by a Lagos State High Court.
The court also said it could not restrain the EFCC from inviting or prosecuting the applicants.
The Commission had in January filed a 40-count charge against Mr. Ekpemukpolo, ex-Director General of the Nigeria Maritime Administration and Safety Agency (NIMASA), Patrick Akpobolokemi and others over the alleged multibillion fraud at the agency.
Others charged alongside them are Global West Vessel Specialist Ltd, Odimiri Electrical Ltd, Kime Engozu, Boloboere Property and Estate Ltd, Rex Elem, Destre Consult Ltd, Gregory Mbonu, and Captain Warredi Enisuoh.
While Mr. Akpobolokemi has been appearing in court to answer to the charges, Mr. Ekpemukpolo has consistently shunned the court summons.
A federal court had, on January 14, issued a warrant for the arrest of the former militant leader after
he shunned an invitation to appear before the court.
On February 8, Justice Ibrahim Buba renewed the arrest warrant and a few days later, the EFCC declared Mr. Ekpemupolo wanted.
Mr. Ekpemukpolo however filed a suit challenging the allegations of fraud against him.
In the suit, filed on his behalf by a Lagos-based lawyer, Ebun-Olu Adegboruwa, the former militant leader contended that sections 221 and 306 of the Administration of Criminal Justice Act (ACJA) 2015, which prohibit him from seeking a stay of proceedings in his trial, were infringing on his constitutional rights to fair hearing.
He asked the court to nullify sections 221 and 306 of the ACJA and restrain the FG, EFCC and the Inspector General of Police from deploying those sections of the law against him.