Their submission means a hearing will be convened in the Netherlands on 7 and 8 December, at which the presiding judge, Lord Sutherland, in the presence of the two men, will rule on whether one of the charges should be dropped.
In papers submitted to the High Court in Edinburgh, lawyers for Abdelbaset Ali Mohmed al-Megrahi and Al-Amin Khalifa Fhimah, claim that the charge of conspiracy to murder, which they deny, should be dismissed.
The 180-page defence submission is that the alleged conspiracy took place outside Scotland and therefore does not fall with the jurisdiction of a Scottish court.
Secondly, the defence argues that the indictment is flawed because the other charge of murder and the conspiracy charge are linked. The defence says that this link is "unfair, oppressive and incompetent", since if they are cleared of the murder charge then it would not be fair to pursue the conspiracy charge.
The two men have been held since April at an airbase in the Netherlands where, under an agreement between the United Kingdom and the Libyans, the full trial is due to commence on 2 February before three Scottish judges under Scots law.
The hearing on the legality of the charges could have taken place in Edinburgh, but has had to be moved to the Netherlands because the two men expressed a wish to be present.
The two deny any involvement in the bombing of Pan Am 103, which blew up over Lockerbie in December 1988, killing 270 people. They are expected to blame the killings on a third Lebanese man.