"I can confirm that inspections did commence," said spokesman Mark Gwozdecky, a week after Tripoli said it was giving up weapons of mass destruction,
IAEA chief Muhammad al-Baradai "and his team went to four nuclear sites previously unvisited and all of them were in the Tripoli area", Gwozdecky said.
"Right now, we are continuing our technical discussions with the Libyan authorities to develop a work plan for the days and weeks ahead."
Al-Baradai, director general of the UN nuclear watchdog, and his team, which arrived on Saturday for a three-day visit, met on Sunday with Maatuk Muhammad Maatuk, deputy premier and head of the Libyan nuclear programme.
An IAEA source, who asked not to be named, said of the talks: "We got a detailed briefing in the history of the nuclear activity and we tried to establish a baseline to obtain key documents and maps.
"We tried to lay out a game plan for the coming days to establish sites needed to be visited, what individuals we would like to interview and obtain key documents that would help us to fill in the gaps in our understanding (of the Libyan nuclear programme)".
The source said discussions would continue on Monday and al-Baradai would hold a press conference at 12:00pm GMT.
The IAEA was expected to have started its site visits at the Tajura experimental reactor, 15 kilometres (10 miles) southeast of Tripoli.
Heart of programme
The Tajura site has been under IAEA supervision since 1980 and "is the heart of the Libyan nuclear programme," according to a Western diplomat.
The IAEA was also to have given an impromptu press conference for the international media at 6pm (1600 GMT) in their hotel, but it was called off for what the foreign ministry called "security reasons".
Tripoli had given assurances before the IAEA mission that the visit would take place with good access for the media, but reporters have so far had little contact with the IAEA team or Libyan officials.
On Monday, al-Baradai is to have talks with Prime Minister Shukri Muhammad Ghanim, the IAEA spokesman said, followed by "another rendezvous" which observers said might be an audience with Libyan leader Muammar Qadhafi.
The IAEA chief was to return to his Vienna headquarters later on Monday, Gwozdecky said.
The protocol is the principal means by which the international community keeps its eye on countries which may be trying to build an atomic bomb.
Al-Baradai said he would submit a report to the IAEA board of governors in March.
Qadhafi has surprised many
with his decision to cooperate
His trip comes after Colonel Qadhafi made the surprise announcement that his country was giving up the search for chemical, biological and nuclear arms.
He said the IAEA was aware Libya had imported nuclear equipment and material "that should have been declared to us. There is a question of how much Libya has complied with its verification obligations."
Libyan officials had told the agency their nuclear programme "was at an initial stage and that no production facilities were developed nor has there been any enrichment of uranium," al-Baradai added.
Libya was under international sanctions for years over the 1988 bombing of a US airliner over the Scottish town of Lockerbie that killed 270 people.
But the United Nations lifted its embargo in September after Tripoli agreed to pay 2.7 billion dollars (2.2 billion euros) in compensation and accept responsibility for the bombing, but denied guilt. US sanctions remain in place.