A number of politicians, including some from the president's Republican party, say they are concerned about Hayden because he is a general with close ties to the military. They are also worried by his role in an eavesdropping programme which critics say was a violation of civil rights.
Peter Hoekstra, a Michigan Republican who heads the House of Representatives Intelligence Committee, said: "It sends the wrong signal, I'm not sure he can adapt."
The CIA lost clout when it fell under a newly created director of national intelligence as part of reforms in response to intelligence failures over the September 11 attacks.
Hayden, 61, is the right-hand man of national intelligence director John Negroponte, who was asked to shake up the US spy community after the 2001 attacks on Washington and New York.
From 1999 to 2005, Hayden headed the ultra-secret National Security Agency (NSA), which employs 21,000 agents dedicated to electronic espionage: deciphering electronic messages, eavesdropping on telephone communications and intercepting email.
But despite spending six years as NSA head and then working as Negroponte's deputy, Hayden is first and foremost a career air force officer and an expert in military intelligence.
He cut his teeth in espionage in the early 1980s in Bulgaria, where he worked as an attache at the US embassy in Sofia.
He served in South Korea and moved through high-level jobs at the Pentagon to become the US military's top intelligence officer.
While at the NSA he supervised a controversial programme of warrantless wiretaps after the 2001 attacks. For this reason, his critics say his confirmation process at the US Senate may not be easy.
The surprise resignation on Friday of Porter Goss, whom Hayden replaces, remains unexplained.