In his first public comments on the Bill, President Museveni said homosexuality should not be promoted but warned against taking unlawful action against homosexuals.
The original version of the bill stipulated a death penalty for some homosexual acts.
However, the revised bill dropped the clause that stipulated the penalty.
In Uganda, homosexual acts are illegal and the government is reviewing the Homosexual Bill to define the types of penalties that should be applied should one be found to be a homosexual or engaging in such acts.
BBC's correspondent in Uganda Catherine Byaruhanga said the government has always stressed that the bill was introduced by an individual MP and was not official policy.
The new head of the Anglican Church of Uganda said the President was careful to neither condemn the bill nor openly support it.
"If there are some homosexuals, we shall not kill or persecute them but there should be no promotion of homosexuality,” said President Museveni.
"We cannot accept promotion of homosexuality as if it is a good thing."
Ministers have warned MPs that passing the bill would have implications for foreign relations.
The bill has been condemned by Western donors, who have suggested that aid could be cut if it is passed in its original or reviewed form.
Rebecca Kadaga, the National Assembly Speaker said the bill would be passed as a "Christmas gift" to its advocates.
However, parliament adjourned until January without voting on it.
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