"I don't think that we can achieve a settlement before the trial starts," Thomas told F1 business journalist Christian Sylt.
"During trials settlements are always possible but not before."
A spokesperson for the Munich court, which is set to hear the criminal bribery case in April, confirmed to the Daily Mail that a settlement is one possible outcome.
The spokesperson said that "according to German legal procedure, there is the possibility during the trial to stop the proceedings in return for payment of an agreed sum of money to a charitable institution or the treasury, if the accused, the public prosecutors and also the court agrees with it".
Sylt said the settlement would likely cost billionaire Ecclestone, who has stepped down as a F1 director while the case is pending, somewhere just shy of EUR 300 million.
"Although it is unusual for a court to take money to settle criminal charges, it is perfectly acceptable in Germany," said Sylt.
Ecclestone said: "The judge is in a difficult position. He has locked somebody (Gerhard Gribkowsky) up for eight and a half years.
"He (the judge) said if the prosecutors wanted to, he would give some consideration to doing that (accepting a settlement) but the prosecutors haven't asked."