Reporters were not allowed into the courtroom to hear the charges being read out despite a pledge by Information Minister Mohammad Momani of "transparency" in Jordan's handling of Abu Qatada's retrial on charges that already earned him a life sentence in his absence.
"State security court prosecutors charged Abu Qatada with conspiracy to carry our terrorist acts," a judicial official told AFP.
"He was remanded in judicial custody for 15 days in the Muwaqqar prison," in eastern Jordan, the official added without elaborating.
But Abu Qatada's lawyer Taysir Diab said he would make a bail application on Monday in the light of the not guilty plea.
"Abu Qatada pleaded not guilty. I will appeal tomorrow to the court to release him on bail," Diab told AFP.
Jordanian law gives Abu Qatada the right to a retrial with him present in the dock following his deportation from Britain earlier on Sunday which ended a decade-long legal battle.
Abu Qatada was condemned to death in absentia in 1999 for conspiracy to carry out terror attacks, including on the American school in Amman, but the sentence was immediately commuted to life imprisonment with hard labour.
In 2000, he was sentenced in his absence to 15 years for plotting to carry out terror attacks on tourists in Jordan during millennium celebrations.