Judge Sterling Johnson ruled on Tuesday that prosecutors will not be able to present documents allegedly linking Shaikh Muhammad Ali al-Muayyad to suspected al-Qaida members in Afghanistan and Croatia.
The case of al-Muayyad and his Yemeni assistant Muhammad Zayid - who are charged in federal court in Brooklyn with supporting al-Qaida and the Palestinian resistance group Hamas - is to begin on Thursday.
If convicted, the 56-year-old al-Muayyad could face more than 60 years in prison. Zayid, 31, could also face more than 30 years.
The government had hoped to prove al-Muayyad's ties to al-Qaida leader Usama bin Ladin with address books containing his name and phone number, which were confiscated from suspected al-Qaida fighters being expelled from the former Yugoslavia.
The government also planned to introduce an admission form for an al-Qaida Afghan training camp that used al-Muayyad as a reference.
But the judge called the Croatian evidence "so remote, I am going to preclude the government from using it".
"[The evidence is] so remote, I am going to preclude the government from using it"
Judge Sterling Johnson
He went on to exclude the Afghan evidence, apparently agreeing with a defence argument that the presence of al-Muayyad's name on the form was not sufficient proof of wrongdoing.
"We don't know who put this name in," the judge said.
He also ruled a videotape showing al-Muayyad with a high-ranking Hamas official on the day of an Israeli bombing could not be introduced without the testimony of Muhammad al-Anasi, an FBI informant who recorded it.
The al-Qaida charge was first undermined in November 2004, when al-Anasi, the government's main informant, set himself on fire in front of the White House in a protest against what he called government mistreatment.
Al-Muayyad and Zayid were arrested two years ago in Frankfurt, Germany, after they were recorded discussing a $2.5 million transfer.
Defence attorneys have said the pair were interested only in getting the money to Islamic charities.