He is wanted by the International Criminal Court (ICC) in The Hague on war crimes charges but this case relates to other charges.
Along with an ICC lawyer, he is accused of trading information threatening national security.
The trial was postponed until May as there was no lawyer to represent him.
His co-accused, ICC lawyer Melinda Taylor and another colleague from the International Criminal Court in The Hague, were absent from the courtroom during Thursday's appearance in court in the western town of Zintan.
But Saif al-Islam's appearance was confirmed to the BBC by Libya's deputy attorney general, Taha Baara.
Ms Taylor, an Australian national, and another colleague were arrested and held for three weeks following a visit to Mr Gaddafi in June last year. They were accused of passing letters to him from his former right-hand man and of carrying secret surveillance equipment.
"He is charged with involvement with the ICC delegation which is accused of carrying papers and other things related to the security of the Libyan state," Taha Baara, told Reuters.
According to AP, he is also charged with attempting to escape prison and insulting the nation's new flag.
Saif al-Islam appeared in a courtroom in the western town of Zintan, where he has been held by militiamen since his capture at the end of 2011.
He was considered the most likely successor to Col Gaddafi before the uprising that led to his father's downfall.
Libya has resisted the ICC's request to extradite Saif al-Islam for trial in The Hague, saying it wants to prosecute him at home, where he could face the death penalty.
But there have been numerous official contradictory statements recently over when that trial will begin, and no-one really knows for now, says the BBC's Rana Jawad in Tripoli.
Taha Baara, the deputy attorney general, told the BBC: "The investigation process is almost complete and the investigation file will soon be transferred to a special judicial review committee to be examined. If they have no objections and all is OK it will be handed back to attorney general for final approval."
Saif al-Islam Gaddafi, the son of former leader Col Muammar Gaddafi, has appeared before a court in Libya, the public prosecutor's office has said.