The Deputy Public Health Minister Surapong Suebwong-lee did not give any figures, but said the full extent of the Aids epidemic had been under-reported because relatives of victims in rural areas were reluctant to report the real cause of death.
The minister said he hoped the new findings would ensure that Thailand received a fair share of the new United Nations global Aids fund to fight the disease.
Correspondents say an estimated one million people in Thailand are infected with HIV, the virus which can lead to Aids, out of a population of 60 million.
Rising toll
Mr Surapong told The Nation newspaper: "Village headmen reported most non-accidental deaths as being a result of 'the heart stopped beating'. This led to a misconception that most Thais die of heart disease.
"But we have done a new random survey and found out that the biggest cause of deaths in the rural areas is Aids."
The UN Programme on HIV-Aids (UNAids) office in Bangkok said Aids deaths in Thailand would continue to rise, since there was no cure.
"This is a common trend because Aids has been in the country for more than a decade and everyone knows that at a certain time those who have been infected must die," said country adviser Sompong Charoensuk.
Thailand has the largest number of people with HIV in east Asia.
Prevention campaign
There are thought to be more than a million people working in the sex industry, and the country attracts nearly 10 million foreign visitors every year.
A massive Aids prevention campaign got under way in the early 1990s
But Aids campaigners in Thailand have recently expressed concern that the disease is spreading to new sectors of Thai society, and that the government's resolve to combat the problem may be slipping.