The 50-year-old was cleared of the four most serious criminal charges he faced - being involved in a criminal organisation, fraud, extortion and arson - as part of a judicial investigation into alleged corruption within Greek football.
However, the shipping magnate has been charged with match-fixing along with 27 other people, who include shareholders and officials in several Greek clubs as well as ex-referees and officials of the Greek football association.
In a statement on the Olympiacos website, Marinakis wrote: "The Judicial Council could not reach a unanimous decision, when it found that certain match fixing charges be upheld against me and another 27 persons.
"The 2:1 majority vote will be tested in court, as the chair of the Judicial Council expressed the dissenting view that those charges will have to be dismissed as well.
"I am certain that my innocence with regard to these remaining charges will be demonstrated by the judicial process that will ensue, thus fully exonerating me and vindicating the stated opinion of the chair of the Judicial Council."
Marinakis has also been ordered to stand down as Olympiacos chairman by November 23, but the charges are not believed to affect his freedom to continue his ownership and running of Forest.