Cambodian Foreign Minister Hor Namhong said military officials from both sides would meet Thursday in Thailand to discuss the previous day's clash, which killed at least two Cambodian soldiers and wounded a total of eight from both sides.
Thailand's Prime Minister Somchai Wongsawat pledged to "use peaceful means."
"If there is violence, we have to negotiate," Somchai said.
Wednesday's clash was the first deadly fighting in four months of tensions since Cambodia's Preah Vihear temple was declared a U.N. World Heritage site.
Many Thais feared their country's claim over nearby land would be undermined, and anti-government protesters have pressed their government to take a harder line on the border conflict, seeking to discredit its patriotic credentials. The protesters have sought the ouster of Thailand's ruling party, occupying the grounds of the prime minister's offices for the past two months.
The fighting Wednesday afternoon lasted for about an hour, with each side accusing the other of firing first.
The battle killed at least two Cambodian soldiers and wounded three others, according to Cambodia's Foreign Ministry. Five Thai soldiers were wounded, the Thai army said.
Thailand's Foreign Ministry said Thai soldiers were peacefully patrolling their own territory along the border when Cambodian soldiers shot at them with rocket propelled grenades and submachine guns.
Cambodia's Foreign Ministry accused Thai troops of launching "heavy armed attacks" at three different locations to push back Cambodians from positions inside Cambodian territory.
The fighting was the latest flare-up in a decades-old dispute over a stretch of jungle near the 11th century Preah Vihear temple. The World Court awarded the temple to Cambodia in 1962, but sovereignty over surrounding land has never been clearly resolved.
Thailand had grudgingly accepted Cambodian sovereignty over the temple with few armed confrontations until this year. But resurgent Thai nationalism sparked by the anti-government protesters put Bangkok authorities under pressure to aggressively pursue the land claims.
Both sides sent hundreds of troops to the area after the UNESCO action, and the dispute also fired a surge of nationalism in Cambodia that helped propel Cambodian Prime Minister Hun Sen to a landslide re-election victory in late July.
Most troops were withdrawn from the area a month later.
But the conflict flared again in recent weeks. A brief gunfight earlier this month wounded one Cambodian and two Thai soldiers. Three days later, two Thai soldiers lost legs when they stepped on land mines in the area.
Charnvit Kasetsiri, a historian who has written extensively on the dispute, said the fight over the temple had long been a proxy for larger conflicts, including World War II and the Cold War, but it had been considered resolved until recently.
"The issue surrounding Preah Vihear temple was over decades ago until it was fanned by nationalist rhetoric for domestic political purposes," he said.
State Department spokesman Sean McCormack said the U.S. would urge both sides to refrain from violence. U.N. Secretary-General Ban Ki-moon also urged restraint and called on the two sides to quickly resolve the dispute.
Thailand's more than 300,000-strong military uses modern American equipment and dwarfs Cambodia's 125,000 less well-equipped troops. Cambodian forces however are well versed in guerrilla warfare after fighting an intense civil war against the communist Khmer Rouge.