Security sources said Seif al-Islam was not present because he was unable to be brought to Tripoli for security reasons.
“We have sent a transfer order to the penal authorities concerned to send those persons implicated in Case Number 630, including Seif al-Islam,” the prosecutor general had told reporters in Tripoli on Wednesday.
Deputy prosecutor general Siddiq al-Sur said that all Libyan prisons come under the authority of the justice ministry.
“If the director of any such establishment refuses to obey orders, he will be pursued by the judiciary,” he said.
Asked about the coincidental court appearances, Sur said only that “the prosecutor general’s office was not officially informed about the date of the trial” in Zintan.
Seen as act of defiance against ICC
The main charges against the suspects in Tripoli include murders committed during the regime’s battle against the revolt that erupted in the eastern city of Benghazi.
Kadhafi was captured and killed by rebels in his hometown of Sirte in October 2011.
Seif al-Islam was seized the following month by a group of former rebels from the mountainous region of Zintan, and has been held there ever since.
The Tripoli trial is seen by some Western observers as an act of defiance against the international court.
A total of 40,000 documents and 4,000 pages of interrogation transcripts will be considered by the court.
The defendants face a string of charges, including the “formation of armed bands to carry out crimes that undermine state security” and “incitation to rape”.
Outside the Tripoli complex on Thursday, several dozen relatives of victims of the 1996 Abu Slim jail massacre allegedly ordered by Senussi staged a protest.
“Death to the assassin!” read placards held by the demonstrators.
Lawyers leaving the compound after the hearing were also subjected to a torrent of abuse.
“You’re all traitors! How could you defend these killers?” demanded one enraged woman demonstrator.