CIA chief backs rendition flights
Mr Hayden staunchly defended "special methods of questioning"
Gen Hayden said programmes such as extraordinary rendition produced what he said was irreplaceable intelligence.
Under the programme, terror suspects are transported to secret prisons in countries with less stringent interrogation rules.
Mr Hayden, speaking in Chicago, said the leads gained justified rendition.
"The irreplaceable nature of that intelligence is the sole reason why we have what I admit freely is a very controversial programme."
The CIA had produced thousands of intelligence reports from the "fewer than 100 hardened terrorists" detained since 2002, Mr Hayden told the Chicago Council on Global Affairs.
His comments came as President George Bush's nominee for US attorney general came under fire for his position on interrogation techniques.
Nominee Michael Mukasey condemned one technique, water-boarding, as "repugnant" and possibly "over the line," but declined to explicitly rule it out as torture, saying he could not speculate on classified procedures.
Water-boarding simulates drowning by immobilizing a prisoner with his head lower than his feet and pouring water over his face.
Leading Democrats in the Senate have threatened to block Mr Mukasey's confirmation if he does not explicitly rule out water-boarding as illegal.
When asked to comment about Mr Mukasey's statement, Mr Hayden avoided a clear answer."Judge Mukasey cannot nor can I answer your question in the abstract. I need to understand the totality of the circumstances in which this question is being posed before I can give you an answer," he said