"I have directed our agency personnel to take charge of the decommissioning process and have further directed that the contracts for site security be promptly terminated," he said.
During the "war on terror" waged by George Bush, the former US president, suspects were captured by security services and taken by CIA planes to a global network of secret prisons.
|Khaled Sheikh Mohammed was among those
held at a CIA secret prison [EPA]
In January, Barack Obama, Bush's successor, ordered that harsh interrogations of suspects be ended and secret detention sites closed.
The agency would also end the contracts of private security firms employed at the so-called "black sites", Panetta said.
Panetta said the CIA would continue to question suspects but that it would use "a dialogue style of questioning that is fully consistent with the interrogation approaches authorised and listed in the Army Field Manual," which bans harsh techniques.
"CIA officers do not tolerate, and will continue to promptly report, any inappropriate behaviour or allegations of abuse.
"That holds true whether a suspect is in the custody of an American partner or a foreign liaison service," he said.
"No CIA contractors will conduct interrogations," Panetta added.
The CIA has acknowledged that Khalid Sheikh Mohammed, who has been accused of plotting the September 11, 2001 attacks against the US, and al-Qaeda suspects Abu Zubayhda and Abd al-Rahim al-Nishiri, were subjected to harsh interrogations at secret prisons.
The three suspects were subjected to waterboarding, a technique designed to induce panic and trigger sensations akin to drowning widely condemned as a form of torture.
If more prisoners were detained, they would be interrogated by agency employees and handed over quickly to their home country or to a country with a legal claim on them, Panetta said.