Prasert Thongcharoen, adviser to the Thailand Disease Control Department, said two of four babies the department had tested had been found to have microcephaly.
"The other two -- one was born already and another baby is due to be born soon -- both have microcephaly conditions but we can't confirm if they are definitely from Zika virus."
Babies with microcephaly are born with small heads to women who contract the mosquito-born Zika virus while pregnant.
Officials declined to reveal where the babies and mothers who had contracted the virus were located in the country.
Thailand is not the only country in Asia to report cases of Zika. Singapore has also seen widespread transmission.
In February 2016, the World Health Organization announced a global state of emergency over Zika, predicting as many as four million cases by the end of the year.
The US Center of Disease Control and Prevention (CDC) advised pregnant women on Thursday to avoid nonessential travel to 11 Southeast Asian countries owing to the possible risk of contracting the Zika virus.
The countries include Brunei, Cambodia, Myanmar, Indonesia, Laos, Malaysia, Maldives, Philippines, Thailand, East Timor and Vietnam.
"The level of risk for Zika virus infection in these countries is unknown, but it is likely lower (but not zero) than in areas where Zika is newly introduced and spreading widely," the CDC said.
According to the World Health Organization and the CDC, the Zika virus is circulating in at least 60 countries.
Thongcharoen stressed it was important that countries stay transparent about the number of Zika cases in their country.
Around 30 pregnant women, who have tested positive for Zika, are on Thailand's watch list. Eight out of the 30 have already given birth and and their babies did not have microcephaly.
Thongcharoen said that Zika tests had been conducted more regularly in Thailand. More than 10,000 people were tested this year and about 300 Zika cases discovered.
The ministry also said that one man who had contracted Zika, suffered from Guillain-Barré -- a syndrome that affects the body's nervous system. Thongcharoen said the man had breathing difficulties and lost strength in his limbs. He has since recovered.