ACM Sukumpol led the Thai delegation for a luncheon meeting with his Cambodian counterpart, Gen Tea Banh, on the border at Preah Vihear, the site of an ancient Khmer-Hindu temple.
Both sides promised to respect the ruling of the International Court of Justice (ICJ) later this year, he said.
ACM Sukumpol said the meeting did not imply any recognition by Thailand that the disputed area immediately adjoining the temple was part of Cambodia.
The two ministers also agreed to settle border disputes through peaceful measures instead of using force, he said.
The meeting was held at the temple over the objections of the Thai Foreign Ministry, which argued it could put Thailand at a disadvantage in the legal dispute between the two countries over the disputed border area.
The world court ruled in 1962 that the Preah Vihear temple ruins were part of Cambodia.
Phnom Penh asked the ICJ in 2011 to interpret its 1962 judgement and clarify ownership of the land immediately adjoining the ruins.
The two parties will present verbal arguments on April 15-19, with a ruling due in October.
Democrat Party leader Abhisit Vejjajiva on Tuesday warned of possible repercussions of the meeting of the two ministers at Preah Vihear, which is called Phra Viharn in Thailand.
He said Cambodia could use the talks to substantiate its claim over the 4.6 square kilometres in dispute.
The opposition leader said he did not oppose talks with Cambodia, but the government should realise that meetings with Cambodia could have an impact on Thailand’s claim.
Relations between Thailand and Cambodia have improved since the Pheu Thai Party backed by former prime minister Thaksin Shinawatra took power in 2011.