At least 36,000 people were displaced on 23-24 April amid fresh fighting along the Thai-Cambodian border, officials say.
The two countries are at loggerheads over ownership of an 11th century Hindu temple, registered as a UN World Heritage Site in 2008.
Each side accused the other of firing rockets and mortars over disputed territory along their 798km border, forcing civilians to flee the area.
Cambodia's Defence Ministry alleges that Thailand fired heavy weapons more than 21km into Cambodian territory.
In a shelter in the town of Samraong, Dee Savi, 46, said she fled with her family after mortar fire near her village, Sambor Meah.
"I couldn't continue farming. It became too dangerous for me and my children. We had to escape," she said.
Kim Bonatha, 59, a doctor from Phnom Penh's Calmette Hospital, who has been treating displaced civilians sheltered in a pagoda in Samraong, said diarrhoea and fever were already becoming a source of concern.
Stephane de Geef, with Jesuit Relief Services, an international Catholic NGO with an office in Cambodia, said there could have been dozens of civilians casualties if not for the evacuation.
Nearly 10,000 Cambodians were relocated to temporary shelters away from the fighting, according to the government's National Disaster Management Committee.
Thai government spokesman Panitan Wattanayagorn said Cambodian fire fell "more than several kilometres" inside Thailand.
At least 26,000 Thai civilians were evacuated from border communities in Buriram and Surin provinces and are now being housed in temporary shelters, he said.
Each side blamed the other for initiating the violence, in which 12 soldiers have reportedly died and dozens been injured since fighting erupted again on 22 April.
In statements, Cambodia's Foreign Ministry said Thai troops launched a "fierce armed offensive", and Thailand's Foreign Ministry alleged Cambodian troops prompted the flare-up with an "unprovoked attack".
Recent arrivals to Samraong Cambodia accused Thailand of firing toxic gas into Cambodian territory, though independent reports from civic groups suggest the smoke plumes came from exploding mortars.
However, claims that the Thai military used cluster munitions during fighting in early February have been corroborated by several NGOs, including the UK-based Cluster Munition Coalition.
Civic groups urged Thailand as well as Cambodia to sign the Convention on Cluster Munitions, an accord supported by 108 countries to outlaw the weapons, which are especially dangerous to civilians because they scatter over a vast area.
"Rise above politics"
Each side has accused the other of exploiting the conflict for political gain.
In his weekly televised address, Thai Prime Minister Abhisit Vejjajiva said Cambodia wished to attract international intervention by intensifying "the conflict so violently that the dispute can no longer be solved at the bilateral level".
In a letter to the UN Security Council, Cambodian Foreign Minister Hor Namhong said Thailand's argument that bilateral negotiations were more productive was "a pretext for using its larger and materially more sophisticated armed forces against Cambodia".
Emma Leslie, director of the Centre for Peace and Conflict Studies, a Phnom Penh-based NGO, said political gamesmanship needed to be put aside in the interests of affected civilians.
"This is the moment for Thai and Cambodian leaders to rise above politics, and bring together two nations with shared history, culture and religious traditions," she told IRIN by email.
"The welfare of the Thai and Khmer people along the border is paramount, and the peace and prosperity for border communities should be the primary concern of decision-makers in Bangkok and Phnom Penh."
On 23 April, UN Secretary-General Ban Ki-moon called on both sides to exercise maximum restraint and an effective and verifiable ceasefire.