The judge ruled the funds would remain in the small European country until a ruling was delivered in a separate case.
"Iran's frozen money in Luxembourg belongs to the period before the (nuclear) negotiations and Iran's (central bank) lawyers are engaged in consultations to obtain it," said deputy foreign minister Majid Takht Ravanchi.
A New York judge ordered Iran to pay $7 billion to the families and estates of victims in 2012 - arguing that Tehran had assisted al-Qaeda in the attack.
The court heard how Iran had allowed the 9/11 bombers to travel through its country on their way to carry out the attack.
Tehran refuses to pay the requested damages however as it does not accept the accusation.
Billions of dollars of Iranian funds abroad were frozen by European and American institutions as a means of pushing Iran to sign an international nuclear deal.Iran is looking to unfreeze the $1.6 billion held by Clearstream clearing house, based in Luxembourg.