George Bush, the US president, gave no explanation for Goss's resignation, and instead praised the former member of Congress from Florida for his candid advice.
The announcement was made at a hastily arranged event in the Oval Office on Friday attended by Goss and John Negroponte, director of national intelligence.
"Porter's tenure at the CIA was one of transition. He's helped this agency become integrated into the intelligence community. That was a tough job. He's led ably," Bush said.
The CIA fell under a newly created director of national intelligence as part of reforms enacted after intelligence failures related to the attacks on the World Trade Centre and Pentagon in 2001.
Some bureaucratic wrangling resulted as the new intelligence arm sought to assert itself over the CIA and met some opposition from within its ranks.
"I'm confident that his successor will continue reforms that he's put in place and as a result, this country will be more secure," Bush said.
Goss, brought in after George Tenet resigned in the face of mounting criticism of intelligence failures over the Iraq war, said he would like to report that the CIA is "on a very even keel, it's sailing well".
Bush gave no explanation for
"I honestly believe that we have improved dramatically your goals for our nation's intelligence capabilities, which are, in fact, the things I think are keeping us very safe," he said.
There was talk among intelligence analysts in Washington that Goss had been asked to resign by Negroponte, but there was no immediate confirmation.
A former CIA agent, who spoke on condition of anonymity, expressed relief at news of the resignation.
"Thank God," he said. "It's gotten so bad there, it's just a charade at the moment. There's no senior leadership."
Another intelligence source said: "You have to know how to transform the agency without making an enemy of it."
Administration officials told CNN on Friday that Michael Hayden, principal deputy director of national intelligence, would replace Goss. Sources also told The New York Times and Time magazine websites that Hayden was a leading candidate for the post.