Cambodia ordered the first secretary of the Thai Embassy to leave Phnom Penh, and Thailand responded in kind.
The move follows the appointment of Mr Thaksin as an economics adviser to the Cambodian government.
Cambodia's foreign affairs ministry spokesman, Koy Kuong, said Phnom Penh expelled the Thai diplomat first and Thailand "responded by asking our first secretary to leave their country within the next 48 hours".
Mr Thaksin was ousted in a military coup in 2006 and has been living in exile ever since. He has been sentenced in his absence to a two-year jail term in Thailand in a conflict of interest case.
But Cambodia has refused an extradition request from Bangkok, saying the charges against him are politically motivated.
Relations between Thailand and Cambodia are already strained. In recent months there has been a series of disputes centred around the 11th-century Preah Vihear temple complex near the border between the two countries.