By Zachary Fagenson

MIAMI (Reuters) - A U.S. federal judge in Miami re-sentenced Jose Padilla on Tuesday to 21 years for a 2007 terrorism conviction after an appeals court deemed the original 17-year sentence too lenient.

Padilla, an al Qaeda recruit and the first U.S. citizen labeled an enemy combatant, was convicted on charges of conspiracy to murder, kidnap and maim people abroad, as well as providing material support for terrorism.

Federal prosecutors agreed not to seek more than 30 years in prison for Padilla as long as his lawyers did not introduce records related to alleged harsh conditions he endured during the 3-1/2 years spent in a South Carolina military prison.

"There are certain things we know and don't know about how Mr. Padilla was held," U.S. District Judge Marcia Cooke said on Tuesday before handing down the stiffer sentence.

Padilla sat shackled in a khaki jumpsuit and did not speak during the two-hour hearing. Under his new sentence, Cooke also ordered Padilla remain held in a super-maximum security prison.

Padilla's mother Estela Lebron, who in 2012 mounted a failed effort to sue former Defense Secretary Donald Rumsfeld and high-ranking military officials for violating the U.S. constitution, rebuked the government.

"Washington, D.C., George Bush, Barack Obama, all of the judges ... they know that my son was tortured," she said, referring to the U.S. president and his predecessor.

Cooke had delayed Padilla's re-sentencing many times as lawyers wrangled over his long criminal history and classified documents.

"His actual involvement in jihad, his actual training, sets him apart," said Assistant U.S. Attorney Richard Del Toro.

But Padilla's lawyer Michael Caruso, a federal public defender, said recruiters for extremist groups lied to Padilla, presenting jihad as defending Muslims under attack.

Padilla, a former Chicago gang member who attended a south Florida mosque, converted to Islam in the mid-1990s after a troubled childhood, his brother Tomas Texidor said in court.

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"He's not the man you think he is," Texidor said, fighting back tears.

Padilla was arrested in 2002 as he returned to Chicago from abroad. Prosecutors said he had spent time at a military training camp in Afghanistan.

He was accused of plotting to detonate a radioactive "dirty bomb" in a U.S. city, but was never charged with that. Then-President George W. Bush ordered him held as an enemy combatant and interrogated in a South Carolina military prison.

Prosecutors later argued Padilla deserved a life sentence for his 2007 conviction, but Cooke rejected that sentence because Padilla did not commit acts of terrorism on U.S. soil, or attacks on officials or a plot to overthrow the U.S. government.

An appeals court ruled in 2011 that the 17-year sentence he ultimately received was not severe enough.

In a 2012 appeal which was rejected by the U.S. Supreme Court, Padilla said he was held in isolation for more than three years at the military prison, shackled for hours in painful "stress" positions and subjected to lengthy bouts of blinding light followed by total darkness.

(Writing by David Adams; editing by Colleen Jenkins, G Crosse and Doina Chiacu)