MIAMI — Convicted al-Qaida terrorism plotter Jose Padilla, a U.S. citizen jailed for years as an enemy combatant, was handed a new 21-year prison sentence Tuesday because an appeals court determined his previous 17-year term was too lenient.

A jury found the Brooklyn-born Padilla guilty in 2007 on charges of supporting al-Qaida and terrorism conspiracy, which carried a possible life sentence. Evidence showed he attended an al-Qaida terrorist camp in Afghanistan before returning to the U.S. in May 2002 on what authorities originally claimed was a mission to detonate a radioactive “dirty bomb” in a major city. Those accusations were later discarded when the “mission” was deemed only a sketchy idea.

Over Justice Department objections, U.S. District Judge Marcia Cooke originally gave Padilla credit for his three-plus years in harsh Pentagon custody at a Navy brig in South Carolina. The new sentence essentially takes away the credit for those years. She rejected prosecutors’ request for a 30-year term.

Cooke, an appointee of President George W. Bush, whose administration approved Padilla’s treatment, said she remained concerned that he had been held for so long without criminal charge, had almost no access to a lawyer and under conditions few U.S. citizens have experienced in this country.

“I was then, and am now, dismayed by the harshness of Mr. Padilla’s prior confinement,” Cooke said.

Assistant U.S. Attorney Brian Frazier said the government may appeal this new sentence as well.

U.S. officials have long rejected Padilla’s claims that while in the brig he was forced to stand in painful stress positions, given LSD or other drugs as “truth serum,” deprived of sleep and subjected to loud noises, extreme heat and cold and noxious odors. But Assistant U.S. Attorney Ricardo Del Toro acknowledged that Padilla “was not treated kindly” as a suspected al-Qaida soldier.

“I’m not arguing to the court that they (brig conditions) weren’t harsh in the general sense,” Del Toro said.

Padilla’s attorney, Michael Caruso, said the years of isolation and interrogation had left Padilla “sunk into a pit of hopelessness and despair.” During Tuesday’s hearing, Padilla sat perfectly still with head bowed looking at an empty tabletop, declining Cooke’s offer to speak in his own behalf.

His mother, Estella Lebron, called the case against Padilla “fabricated from the beginning.”

“The way they treated my son, they don’t treat an animal in America or anywhere else,” she said.

The new sentence was imposed because the 11th U.S. Circuit Court of Appeals in 2011 determined that Cooke erred in giving Padilla credit for the brig years and also failed to properly account for his “heightened risk of dangerousness” due to the al-Qaida training. In addition, the appeals judges ruled that Padilla — a former Chicago “Latin Kings” gang member — deserved a longer sentence because of his 17 previous arrests.

Padilla, 43, was arrested in 2002 at Chicago’s O’Hare International Airport during the tense months after the 9/11 attacks and accused of the “dirty bomb” mission. It later emerged through U.S. interrogation of other al-Qaida suspects that the “mission” was only a sketchy idea, and those claims never surfaced in the South Florida terrorism case.

Before his 2005 indictment, Padilla’s attorneys challenged the right of the Bush administration to continue holding a U.S. citizen like him as a combatant without charge. Because he was finally charged criminally, the U.S. Supreme Court never got a chance to rule on the question.

Trial testimony showed that Padilla had begun frequenting a Florida mosque where his co-defendant, Adham Hassoun, was recruiting fighters for Muslim jihad overseas. Padilla eventually traveled to Egypt and on to Afghanistan. A key piece of evidence against him was his name on an al-Qaida form listing attendees at the al-Farook terrorism training camp.

Hassoun and a third defendant, Islamist propagandist Kifah Jayyousi, where also convicted in the case. Hassoun is serving 15 years and Jayyousi 12 years. They are scheduled for release in 2017, another factor in Cooke’s decision not to give Padilla a longer sentence.

“Mr. Hassoun and Mr. Jayyousi clearly manipulated Mr. Padilla,” she said.