Annette Lu made the controversial comments on television at an AIDS awareness event on Monday.
“God felt it’s time to mete out punishment, or there would not be any difference between men and animals,” Lu said, urging the public to practise safe sex.
The Presidential Office expressed regret over the report, saying the comments had been misinterpreted.
“Instead, Vice President Lu asked the public not to discriminate against AIDS patients,” the office said in a statement.
But the remarks were severely condemned by local gay rights groups.
“AIDS and homosexuals have been wrongly blamed… If she really said that, then she would be just one of those who attempted to smear the image of homosexuals,” Chan Ming-chou of Taiwan Gay and Lesbian Association told AFP.
Parliamentarian Chou Hsi-wei from the opposition People First Party also blasted Lu, who is the convenor of a human rights consultation group that falls under the Presidential Office.
“How can our vice president say this? Just think – some of the AIDS victims are children,” the legislator said.
Even members of the vice president’s own Democratic Progressive Party (DPP) appeared embarrassed.
“She should not have said [it]… but I think it was a slip of the tongue,” DPP parliamentarian Lin Yu-sheng said.
Taiwan is generally tolerant of homosexuality. Its cabinet is drafting a bill to legalise “gay marriages” and recognise the right of homosexual couples to adopt children which, if approved, would make the island the first region in Asia to legalise same-sex marriages.
The final draft of the bill is expected to be ready for parliamentary review this month.
The island has a low rate of AIDS infection compared with other countries in the Asia-Pacific region, where AIDS kills a person every minute, according to the World Health Organisation.
A total of 5550 people in Taiwan, including 5125 Taiwan citizens and 425 foreigners, were listed as AIDS virus carriers from 1984 to 30 November, according to the Centres for Disease Control.
It says 907 domestic AIDS patients have died of the disease.