Gen Chavalit said Hun Sen was full of praise for Thaksin and expressed sympathy for the "political injustice" he suffered in Thailand.
"He [Hun Sen] feels Thaksin is not fairly treated, politically," Gen Chavalit said. "Despite having contributed to the country, he has no place to stay. Hun Sen is in pain even though he is not a Thai.
"So he feels the need to make it publicly known he and Thaksin have always been friends."
Gen Chavalit quoted Hun Sen as saying "Thaksin is welcomed in Cambodia".
AFP also reported that state-run TVK said the Cambodian prime minister made the invitation during a private meeting with Gen Chavalit. If "former Thai prime minister Thaksin Shinawatra wishes to travel to Cambodia anytime ... ", the television channel reported.
Thaksin spends most of his time in Dubai since fleeing the country.
Gen Chavalit's one-day visit to Phnom Penh was at the invitation of the Cambodian prime minister. He was greeted by Cambodian Defence Minister Tea Banh.
The Cambodian prime minister also sought to bolster relations between his ruling Cambodian People's Party and Puea Thai, an official in the Chavalit delegate said.
Gen Tea Banh was assigned as a coordinator for the Cambodian People's Party while Gen Wichit Yathip was named a coordinator for the Thai side, the official said.
Hun Sen's invitation came days after Gen Chavalit joined the opposition party - a reincarnation of the two dissolved People Power and Thai Rak Thai parties.
Gen Chavalit's joining of Puea Thai was followed by a parade of some 50 former classmates of Thaksin from Class 10 of the Armed Forces Academies Preparatory School to the party.
Hun Sen's remarks are likely to frustrate the Thai government which has tried to establish Thaksin's whereabouts to facilitate its attempt to extradite him and make him serve his two-year jail term.
The remarks are also considered untimely ahead of the Asean summit which starts tomorrow.
Gen Chavalit played down speculation that Hun Sen's comments could cause a further deterioration in relations between the two countries. Border tensions have simmered in past months over the Preah Vihear temple issue. Both countries lay claim to the overlapping areas of 4.6 square kilometres near the temple ruins.
"The country's disputes will have to be dealt with. The relationship between Hun Sen and Thaksin is another matter," Gen Chavalit said.
Prime Minister Abhisit Vejjajiva said before Gen Chavalit's departure to Phnom Penh the meeting between the Puea Thai chairman and Hun Sen was "normal".
"Such a meeting is normal," he said. "I have once visited the Cambodian government [as part of] an opposition party," the prime minister said.
Mr Abhisit said he did not think the government's authority would be overshadowed by the opposition because it was clearly known who was the government and who was on the opposition bench.
Gen Chavalit said the government should not be concerned about his trip. It was a private visit, not a state affair, he said.