A decades-old border dispute between the Southeast Asian nations erupted into military clashes several times last year, with fighting in December killing dozens of people and displacing around one million on both sides.
The two countries agreed a fragile truce on December 27, ending three weeks of clashes.
"Cambodia has violated the ceasefire" on Tuesday morning, the Thai army said in a statement, accusing Cambodian forces of firing mortar rounds into Thailand's Ubon Ratchathani province.
One soldier was wounded by shrapnel, it added.
The Thai army said in a later statement that the Cambodian side had contacted a Thai military unit and claimed "there was no intention to fire into Thai territory", adding "the incident was caused by an operational error by Cambodian personnel".
The Thai military said it warned Cambodian forces to exercise caution, stressing if a similar incident occurred, Thailand may need to retaliate.
Cambodia's defence ministry spokeswoman Maly Socheata said two Cambodian soldiers were injured, one severely, on Tuesday morning in Cambodia's Preah Vihear province, which sits opposite Thailand's Ubon Ratchathani.
While Cambodian forces were performing "organization and orderliness" duties, "an explosion occurred from a pile of garbage", she said, resulting in the two injured soldiers being hospitalised.
Socheata did not mention the strike alleged by Thailand, but said both nations' border coordination teams had consulted on the incident involving the Cambodian soldiers and addressed the matter.
The explosion occurred in a frontier region known as the Emerald Triangle, Socheata added where the borders of both countries and Laos meet.
In May, a Cambodian soldier was killed in a firefight with Thai troops in the area, reigniting the border conflict.
- 'An accident' -
Thailand's Prime Minister Anutin Charnvirakul said his government had lodged a protest with Phnom Penh, stating "the truce was violated".
"At the military-to-military level, we have been told the incident was an accident, but we are seeking clarification on how responsibility will be taken," Anutin told reporters in Bangkok.
Charnvirakul added that Thailand had the "capability to respond" to Cambodia, which is vastly outgunned by its neighbour.
The nations' long-standing conflict stems from a dispute over the colonial-era demarcation of their 800-kilometre (500-mile) border, where both sides claim territory and centuries-old temple ruins.
Under the December truce, Cambodia and Thailand pledged to cease fire, freeze troop movements and cooperate on demining efforts along their border.
On December 31, Bangkok released 18 Cambodian soldiers held since July when border clashes that month killed dozens of people.
Thailand's foreign ministry said their release was "a demonstration of goodwill and confidence-building".
Phnom Penh said last week it remained "hopeful" that their return would "significantly contribute to building mutual trust".
The United States, China and Malaysia had brokered a truce to end the fighting between Cambodia and Thailand in July, but that ceasefire was short-lived.
- Disputed border -
On Saturday, one week after the December truce went into effect, Cambodia called on Thailand to pull out its forces from several border areas Phnom Penh claims as its own.
The Thai military has rejected claims it had used force to seize Cambodia territory, insisting its forces were present in areas that had always belonged to Thailand.
While the two nations agreed late last month to stop fighting, they still need to resolve the demarcation of their disputed border.
Cambodia's defence ministry said in a statement Tuesday that Phnom Penh had proposed a bilateral border committee meeting with Thai counterparts to be held in Cambodia's Siem Reap province this month.
Bangkok has said previously that meetings to discuss border surveying and demarcation may need to be held by Thailand's next government, following elections scheduled for February 8.
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