The Thai Red Cross Society says it does not discriminate against gay people, but the policy not to accept them as blood donors is internationally applied.
National Blood Centre director Soisaang Pikulsod, discussed the topic at the 21st Academic Annual Meeting of the National Blood Centre held on Wednesday.
Dr Soisaang's comment came after a video clip of three young people criticising the Red Cross Society for refusing to accept blood donations from the third gender was posted on Youtube.
She said the Thai Red Cross has been dealing with this problem for over five years and she has explained the issue to the National Human Rights Commission several times.
She insisted that the organisation does not discriminate based on gender but it has an international policy to classify them as a HIV high risk group.
She said the policy is still enforced worldwide in the interests of patients in need of uninfected blood.
According to the statistic made by the National Blood Centre, 2% of total blood donations were found infected with HIV or Hepatitis and almost 100% of the infected blood was donated by gay men, she said.
Dr Soisaang said the National Blood Centre contacts donors after detecting these viruses in the blood to inform them and to re-interview them.
"We usually find out that they lied in filling out their forms the first time, usually saying that they are straight or do not have unprotected sex," she said.
She said she does not approve of the idea, "if it is not usable just throw it away". This would be sinful.
It was also difficult to detect the HIV virus in the blood of people who were recently infected, and there was no test that could detect the virus in the blood stream in the first 11 days after being infected.
She said that in 2012, only about 80% of blood donations countrywide were subjected to Nucleic Acid Amplification Technology (NAT) tests to detect HIV.
Dr Soisaang said 64% of the tests are done at the National Blood Centre and 16% at public hospitals in Bangkok and other provinces.
She said the remaining 20% of blood donations that are not tested are at risk of being infected, so precautionary measures must be taken to reduce the risk as far as possible.