Presiding judge Klaus Ruehle gave the order on Thursday after police submitted evidence of a claim by an informant that Mzudi was not involved in the deadly hijackings.
However, the case against the 30-year-old Moroccan is continuing and the charges have not been lifted. He is accused of accessory to the murder of more than 3000 people and membership of a "terrorist" organisation.
Earlier, the federal crime office (BKA) told the court in a letter that an unidentified informant claimed Mzudi was not part of the plot.
The source reportedly said only four people in an al-Qaida cell in Hamburg, northern Germany, knew of the plan for the 2001 attacks.
He said these were three of the later hijackers and Ramzi bin al-Shibh, an alleged senior al-Qaida operative now in US custody.
Mzudi and Mutassadiq prayed at
Hamburg's al-Quds mosque
The BKA warned that the source had provided conflicting information in the past and said al-Qaida members were schooled in how to confuse interrogators and provide misleading information.
Meanwhile, a lawyer for Moroccan Munir al-Mutassadiq, convicted and jailed in Germany for abetting the September 11 attacks, said on Thursday he would also demand his immediate release.
"We will make an immediate move to get him out, this is clear," lawyer Josef Graessle-Muenscher said.
Al-Mutassadiq was sentenced to 15 years in jail last February for plotting with the September 11 hijackers.