Magistrate Graham Mowbray made the comment while hearing an application in the Federal Magistrates Court in Canberra to extend an interim "control order" placed on Mr Thomas after his conviction on terrorism charges was overturned on appeal.
The control order restricts Mr Thomas's movements, imposes a curfew and prohibits him from contacting a list of people - including Bin Laden, whom he is alleged to have met while training in Afghanistan.
Political commentators have also scorned the inclusion of Bin Laden on the list, suggesting the government should instead be delighted if Mr Thomas could lead them to the man the US has been hunting for five years.
Mr Thomas' lawyer Lex Lasry described the situation as "ridiculous", saying the list also included 13 people who were either dead or in custody at the US military prison at Guantanamo Bay in Cuba.
But lawyer Tom Howe, representing the government, disagreed with criticism of the inclusion of Bin Laden's name, saying Mr Thomas had allegedly met Bin Laden three times.
"We couldn't safely presume there is absolutely no possibility of contact," Mr Howe told the court.
The government used controversial new anti-terror laws for the first time on Monday to place the control order on Mr Thomas after an appeal court overturned his conviction and five-year jail sentence for receiving money and an air ticket from Al-Qaeda.