The rare tour to Iran's main uranium enrichment facility at Natanz and the heavy water installation in Arak was snubbed by Iran's key allies China and Russia, as well as the European Union.
Iran had invited several envoys to the Vienna-based International Atomic Energy Agency (IAEA) as well as Hungary, the holder of the European Union's rotating presidency, to take part in the tour.
However, the United States, Britain, France and Germany were not invited, according to diplomatic sources.
"The NAM (Non-Aligned Movement) troika, the Group of 77 members, the Arab League, Syria, Venezuela and Oman, are participating in the visit," Iran's IAEA envoy, Ali Asghar Soltanieh, told Fars news agency.
State news agency IRNA reported that the team had left for Arak to tour the still-unfinished facility.
Russia and China appear to have declined to participate in the visit, as indicated by comments from their capitals. "(China's) Vienna representative is still at home right now, so it will be difficult for him to go," Beijing's foreign ministry spokesman Hong Lei said on Friday.
Russian Foreign Minister Sergei Lavrov said on Thursday that while Iran's invitation "deserved attention," such a trip could not replace IAEA inspections, indicating Moscow would refrain from participating.
The European Union declined the invitation outright, saying the IAEA "are the people who have to inspect the Iranian nuclear facilities."
Soltanieh said the EU had missed a "historic opportunity."
"As a goodwill gesture, the Islamic Republic of Iran invited some countries, including the European Union. But it (EU) did not use this historic opportunity of cooperation and witnessing the Islamic republic's peaceful activities," IRNA quoted him as saying by IRNA.
"(But) we respect their decision."
Meanwhile, foreign minister and atomic chief Ali Akbar Salehi said Iran would reveal new achievements during the visit to the Arak facility.
"Today, at the heavy water installation in Arak, we will unveil several new nuclear achievements in the field of medicine," he said.
"This achievement will be unveiled in the presence of guests who we have invited from different countries and international organisations."
Iran has pitched the trip as a confidence-building measure.
"No country in the world will show its nuclear installations to others and this is a sign that Iran's nuclear activities are peaceful," Salehi told ISNA on Friday.
Such visits to Iran's atomic sites are infrequent. The last trip that Tehran arranged for members of the IAEA was in February 2007.
The Iranian move came in the run-up to talks with six world powers at the end of next week in Turkey chaired by EU foreign policy chief Catherine Ashton.
Britain, China, France, Russia, the United States and Germany are to meet with Iran for another round of talks on Tehran's atomic programme in Istanbul on January 21-22.
The previous round of talks, after a 14-month hiatus, was held in Geneva on December 6-7.
Western powers suspect Iran wants to use its uranium enrichment activities to build a nuclear bomb. Tehran denies the charge, insisting its programme is a peaceful effort to produce nuclear energy.
Iran maintains it will not discuss its nuclear dossier in Istanbul, but Ashton has categorically said Tehran's nuclear programme would be part of the discussions.
"I'm very clear that we are coming to discuss the nuclear issue and that is what we will do," Ashton said on Thursday.
Iran is under four sets of UN sanctions over its refusal to suspend uranium enrichment. The most sensitive part of the atomic programme, it can be used not only to make nuclear fuel, but also the fissile material of a bomb.