In the Thai capital Bangkok, Major-General Kanok NetraKaveysana confirmed that there had been a brief firefight early in the morning.
"It was a misunderstanding and it has been resolved," he said.
The fighting erupted a day after a Thai soldier was wounded when he stepped on a landmine near the 900-year-old Preah Vihear temple, where both sides have stationed troops since armed clashes occurred in the area last year.
Tensions flared again last month when 100 Thai troops crossed into a disputed area near the temple and were stopped by Cambodian soldiers.
Preah Vihear, or Khao Phra Viharn as it is known in Thailand, sits on an escarpment that forms the natural border between the two countries and has been a source of tension for generations.
The International Court of Justice awarded it to Cambodia in 1962, but the ruling did not determine the ownership of 4.6sq km of jungle next to the ruins, leaving considerable scope for disagreement between the two countries.