U.S. District Judge Katherine Forrest left the 11-count indictment against Abu Hamza intact, the Courthouse News Service reported.
The indictment alleges that Hamza, who is said to have lost much of his forearms fighting the Soviet occupation of Afghanistan, conspired to detain U.S. nationals in Yemen in 1998.
He allegedly provided a phone to the leader of the Abyan faction of the Islamic Army of Adem.
He also is accused of giving advice to a co-conspirator over the phone about the kidnapping of 16 people, two of whom were U.S. citizens, which took place between Dec. 23 and Dec. 29.
Hamza is also accused of conspiring to create a jihad training camp in Bly, Ore., by stockpiling weapons and ammunition he allegedly received from al-Qaida.
Defense lawyers argued that Hamza could not be charged for advising the kidnappers over the phone, but Forrest issued her decision not to dismiss the complaint Friday.
"There is no requirement that the indictment contain allegations of defendant's presence in the United States ... Rather, the determinative issue is whether defendant's actions were calculated to harm American citizens and interests," she wrote.
Hamza was arrested in England in 2004 and extradited to the United States in 2012.
The trial is set to begin March 31, 2014.