Thailand's army accused Cambodia on Monday of violating a newly signed ceasefire agreement, reached after weeks of deadly border clashes, by flying more than 250 drones over its territory.

The Southeast Asian neighbours agreed to the "immediate" ceasefire on Saturday, pledging to end renewed border clashes that killed dozens of people and displaced more than a million this month.

But the fresh allegation from Bangkok and its threat to reconsider releasing Cambodian soldiers held by Thailand left a sustained truce in doubt, even as their foreign ministers wrapped up two days of talks hosted by China.

The Thai army said on Monday "more than 250 unmanned aerial vehicles (UAVs) were detected flying from the Cambodian side, intruding into Thailand's sovereign territory" on Sunday night, according to a statement.

"Such actions constitute provocation and a violation of measures aimed at reducing tensions, which are inconsistent with the Joint Statement agreed" during a bilateral border committee meeting on Saturday, it said.

The reignited fighting this month spread to nearly every border province on both sides, shattering an earlier truce for which US President Donald Trump took credit.

Under the truce pact signed on Saturday, Cambodia and Thailand agreed to cease fire, freeze troop movements and cooperate on de-mining efforts and combating cybercrime.

They also agreed to allow civilians living in border areas to return home as soon as possible, while Thailand was to return 18 Cambodian soldiers captured in July within 72 hours, if the ceasefire held.

Cambodian Foreign Minister Prak Sokhonn described the drone incident as "a small issue related to flying drones seen by both sides along the border line."

He said on Cambodian state television on Monday that the two sides had discussed the issue and agreed to investigate and "resolve it immediately."

Phnom Penh's defence ministry spokeswoman Maly Socheata later denied any drones had been flown by the Cambodian side because the ministry and provincial authorities on the border had banned such flights.

"We confirm that no such drone launches have occurred," she said in a statement.

Thai army spokesman Winthai Suvaree said in a statement the drone activity reflected "provocative actions" and a "hostile stance toward Thailand," which could affect the security of military personnel and civilians in border areas.

Thailand's army "may need to reconsider its decision regarding the release of 18 Cambodian soldiers, depending on the situation and the behaviour observed," it said.

Five days of border clashes in July killed dozens of people before a truce was brokered by the United States, China and Malaysia, the chair of the Asean regional bloc.

Trump witnessed the signing of a follow-on declaration between Thailand and Cambodia in October but it was broken within weeks, with each side blaming the other for instigating the fresh fighting.

The conflict stems from a territorial dispute over the colonial-era demarcation of the 800-kilometre Thai-Cambodian border, where both sides claim centuries-old temple ruins.

While the two nations agreed on Saturday to stop fighting, they still need to resolve the demarcation of their border. (AFP)