Thailand's army has accused Cambodia of violating a newly signed ceasefire agreement by flying more than 250 drones over its territory.

Thailand and Cambodia 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 the deal in doubt, even as the two nations' foreign ministers wrapped up two days of talks hosted by China aimed at rebuilding trust and improving relations.

The Thai army said "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 added.

Cambodian Defence Minister Tea Seiha signed the peace deal on Saturday with Thai Defense Minister Natthaphon Narkphanit. (AP: AKP)

Cambodia describes drone issue as 'small'

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, the South-East Asian neighbours 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".

In remarks aired on Cambodian state television on Monday, he said the two sides had discussed it and agreed to investigate and "resolve it immediately".

Thai army spokesperson Winthai Suvaree, however, said in its statement that the drone activity reflected "Cambodia's continued provocative actions and 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", the statement added.

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