"I have told the Criminal Investigations Department to look for homosexuals, lock them up and charge them," the New Vision quoted the president as saying.
His comments came at the opening of a meeting on reproductive health.
"God created Adam and Eve," he said. "I did not see God creating man and man."
President Museveni's comments come two weeks after the widely reported gay marriage of two men in the capital, Kampala.
Poll rejects homosexuality
Under Ugandan law, homosexuals can be charged with "carnal knowledge of another against the order of nature."
Conviction can lead to life imprisonment.
A poll published in the New Vision before the president spoke said that 84% of Kampala residents did not want homosexuality legalised.
The paper said it canvassed 505 male and female people of all ages and educational standards.
The idea that homosexuality is an imported western practice and essentially "un-African" finds echoes in comments made by the Zimbabwean President Robert Mugabe.
Mr Mugabe once described homosexuals as "worse than pigs and dogs".
Country profiles
Protest at 'gay marriage' plans
(31 Jan 99 | Europe)
Gay rights win in South Africa
(09 Oct 98 | Africa)
Homosexual and hated
(12 Aug 98 | Top features)
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