The mass exodus of labourers - who play a key role in Thai industries such as seafood and agriculture but often lack official work permits - comes amid a junta warning of arrest and deportation for illegal foreign workers.
"They're returning en masse like a dam collapsing. They've never come en masse like this before in our history," Kor Sam Saroeut, governor of the northwestern province of Banteay Meanchey where the main border crossing is located, told AFP by telephone.
"They said they are scared of being arrested or shot if they run when Thai authorities check their houses," Saroeut added. "Most of them went to work in Thailand without a work permit."
Sirichan Ngathong, a spokeswoman for Thailand's army which seized power in a coup on May 22, had said Wednesday the junta viewed illegal migrants as a "threat" and they faced arrest and deportation.
But two days later the Thai foreign ministry dismissed "rumours" the army was deporting Cambodian labourers and later today released a new statement citing spokesman Sek Wannamethee as saying: "No crackdown order targeting Cambodian workers had been issued by the NCPO (junta body)."
More than 12,000 migrant workers crossed the border into Cambodia today alone, according to Saroeut, who expects many more to make the journey over the new few days.
Thousands were sheltering from the rain at local Buddhist temples and a market as they waited for transport to their home provinces.
Cambodian authorities have arranged nearly 300 cars and military trucks to ferry workers home from the Aranyaprathet- Poipet border checkpoint but many would have to stay near the site overnight until transport became available, Saroeut said.