The announcement could affect Thailand's key tourism industry, one the kingdom's few economic bright spots under junta rule, with many Western governments warning pregnant women against non-essential travel to Zika-affected areas.
"Two of the three infants (tested) had microcephaly due to the Zika virus," Wicharn Pawan, a disease control official at the Health Ministry told AFP.
The ministry later said tests remain inconclusive as to whether Zika was linked to the third infant's condition.
Zika causes only mild symptoms in most, including fever, sore eyes and a rash.
But pregnant women with the mosquito-borne virus risk giving birth to babies with microcephaly -- a deformation that leads to abnormally small brains and heads.
There is no cure or vaccine for the virus, which has infected more than 1.5 million people in nearly 70 countries since last year, according to WHO, with Brazil the hardest hit.
While Zika has been present in Southeast Asia for years, there has been an uptick in the number of recorded cases in the region in recent months.
Today it urged Southeast Asian countries to strengthen measures aimed at preventing, detecting and responding to the virus.
But it praised the reaction in Thailand where "authorities have been active in detecting and responding," to the Zika virus, according to Dr Poonam Khetrapal Singh, WHO's Regional Director for Southeast Asia in a statement.
This week Thailand's health ministry said it was monitoring 36 pregnant women infected with Zika, three of whom recently gave birth to babies with microcephaly.
Thai virologist Praset Thongcharoen said Friday that "4.3 infants per 100,000", are born with microcephaly in Thailand, twice the global average.
Scientists warned this month that the world should prepare for a "global epidemic" of microcephaly as Zika takes root in new countries.
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