Khodorkovsky and Platon Lebedev, both 43, were sentenced to eight years each for fraud and tax evasion in May 2005.
"It is possible that they may face new charges," Yury Chaika said, adding that it would only happen if there is sufficient evidence.
"Investigations into the main [Yukos] case are continuing," Chaika said. "Some of its numerous episodes are already in court."
Former Yukos security chief Alexei Pichugin was given 24 years in prison for carrying out two murders and organizing an attempted killing.
Prosecutors continue to investigate suspected money laundering in the now bankrupt Yukos Oil Company [RTS: YUKO].
"We know one thing - the Prosecutor General's Office is continuing the pre-trial investigation into separate episodes," Lebedev's lawyer Yevgeny Baru said, adding that it was too early to speak of any new charges.
The prosecutors opened a new probe in the Yukos case in the summer of 2005.
"The question was raised last summer when we were presented with documents extending the deadline for the pre-trial investigation," another lawyer for Lebedev, Konstantin Rivkin, said.
In July 2005, prosecutors told defense lawyers that Lebedev and Khodorkovsky should be taken to a pre-trial detention center to face new charges, but no charges followed.
