
The ministry informed Unesco in March that only the main building of the Preah Vihear temple was inscribed as a world heritage site, where the UN and the World Heritage Committee could work.
The wider promontory, cliff and cave were not included - so Unesco officials could not pass through these areas without Thai permission.
The International Court of Justice ruled in 1962 that Preah Vihear temple belonged to Cambodia but Thailand claims surrounding areas. The disputed area of 4.6 square kilometres has not been demarcated.
To the ministry's concern, experts from the International Councils On Monuments and Sites (ICOMOS) entered the area early last month - but Unesco's assistant director-general for culture, Francoise Riviere, did not inform the Thai embassy in Paris about the mission until April 17.
The group of experts landed by helicopter at the cliff from the Cambodian side and entered the building through the stair channel, and spent two hours at the site, a ministry statement said.
Unesco's Wing said the organisation was aware of Thai concern and very cautious.
"We listen carefully to the comments of Thai officials and I will inform my director here in Bangkok," Wing said after meeting with Virachai.
But he said Unesco staff in Bangkok had no details about the work its experts did in April as it was coordinated by offices in Paris and Phnom Penh.