Charges of violation of the Social Security Systems Law were filed against Defrodo Melanio, owner of Virgin Pearl, for his alleged failure to remit the SSS premiums of the ships 24 crew members.
There has been no word on 22 of the crewmen, while the two others were found dead on Lahad Datu island off the East Malaysian state of Sabah two years ago.
SSS lawyer Evangeline Hernandez filed the case after Melanio failed to submit his counter-affidavit.
Virgin Pearl disappeared a month after it embarked on its maiden voyage from Davao City to Bitung in North Sulawesi, Indonesia.
The ship captain was reportedly last heard on April 5, 1998 seeking help from authorities by radio when the vessel was about to sink in the waters of Sarangani Bay near General Santos City.
Search and rescue operations only yielded the bodies of Carlito Suarez and another crewman. Edith Regalado