At a hearing to rule on the Moroccan's request to be released from jail, Judge Ernst-Rainer Schudt pointed to a March appeals court ruling that the suspect failed to get a fair trial the first time.
Consequently, Schudt said that "in the further course of the proceedings it may have to be considered that ... the question of closing the case will arise," the Hamburg state court said.
It was the first time the court has publicly raised such doubts about the government's case.
Prosecutor Walter Hemberger said the government has no intention of dropping the charges.
El Motassadeq, 29, won a retrial after appeals judges ruled he was unfairly denied testimony from Ramzi Binalshibh, a Yemeni in secret U.S. custody who is believed to have been the Hamburg cell's key contact with al Qaeda.
The Hamburg court heard el Motassadeq's plea for freedom in a closed hearing Friday. It said it would deliberate and issue a ruling next week.
New evidence emerged at the hearing that bolstered the Moroccan's argument that he knew nothing about the plot, the lawyer said.
Graessle-Muenscher said prosecutors on Friday introduced an intercepted letter that suspected cell member Said Bahaji wrote to his mother in 2002.
"In the letter, Bahaji says Mounir didn't know anything," the lawyer said.
German authorities say Bahaji, left Germany shortly before the Sept. 11 attacks and remains on the run.
Hemberger refused to comment on the evidence introduced Friday.
"We made our arguments, they made theirs and now it's up to the court to decide," he said.
El Motassadeq's retrial is scheduled to start June 16.
He was convicted in February 2003 of more than 3,000 counts of accessory to murder and membership in a terrorist organization, and sentenced to the maximum 15 years in prison.
Prosecutors allege he handled financial transactions for cell members to help keep up appearances of a normal student life as they plotted the attacks.
El Motassadeq has acknowledged knowing the cell members but denies any knowledge of the Sept. 11 plot.
U.S. authorities refused to allow Binalshibh to testify at el Motassadeq's trial or to allow German intelligence services to turn over copies of interrogation reports the United States had provided them.
The absence of Binalshibh's testimony also helped bring about the acquittal of el Motassadeq's friend and fellow Moroccan, Abdelghani Mzoudi, on the same charges in February.
Mzoudi's case took a turn toward acquittal when the Hamburg court heard a statement from an unnamed source that only Binalshibh and the suicide hijackers knew of the Sept. 11 plot — an assertion that could exonerate el Motassadeq. The court said it believed the source was Binalshibh himself.