President Barack Obama has instructed officials to consider how countries treat their gay and lesbian populations when making decisions about allocating foreign aid.

In the first US government strategy to deal with human rights abuses against lesbian, gay, bisexual and transgender (LGBT) citizens abroad, a presidential memorandum issued on Tuesday instructs agencies to use foreign aid to promote such rights.

Gay and lesbian lobby groups have reported an increase in human rights abuses across Africa and parts of the Middle East.

Obama is among international leaders who have condemned a bill proposed in Uganda that would make some homosexual acts a crime punishable by death. The Ugandan parliament recently reopened debate on the bill, which had been abandoned after an international outcry.

In a speech in Geneva to mark international human rights day, secretary of state Hillary Clinton backed the presidential directive. "I am not saying that gay people can't or don't commit crimes," she said. "They can and they do. Just like straight people. And when they do, they should be held accountable. But it should never be a crime to be gay."

Clinton has called for greater protection of sexual minorities and the safety of those seeking asylum. In June, she welcomed a UN resolution on equal rights for all, regardless of sexual orientation.

Clinton compared the struggle for gay equality to difficult passages toward women's rights and racial equality, and said a country's cultural or religious traditions are no excuse for discrimination. "Gay rights are human rights, and human rights are gay rights," she said.

Among US measures, the state department will lead a group to direct agencies to provide a "swift and meaningful" response to serious incidents that threaten the human rights of LGBT people abroad, Obama said. Agencies are directed to combat the criminalisation of LGBT status or conduct abroad, protect vulnerable LGBT refugees and asylum seekers, and engage international organisations in the fight against such discrimination. Agencies are instructed to report on progress within 180 days.

Republican presidential hopeful Mitt Romney argued gay rights should not be a test for US engagement abroad. "I will be looking at foreign aid, whether it meets our national security interests and, number two, whether these nations are friends of ours and are willing to be friendly with us in ways when it matters the most," he said on Fox News.

The Texas governor, Rick Perry, went further. "Promoting special rights for gays in foreign countries is not in America's interests and not worth a dime of taxpayers' money," a Perry campaign statement said.

It was unclear whether those countries that target and discriminate against gay and lesbians would have their funding cut.

The latest state department report cites countries including US allies such as Saudi Arabia as having human rights issues over treatment of homosexuals.

The UN Human Rights Council passed the resolution on equal rights for all by a narrow margin, despite strong objections from African and Muslim countries.

While the US, the EU and Brazil backed the effort, the move drew strong criticism from Russia, Saudi Arabia, Nigeria, and Pakistan, among others.

In October this year, USAID made an announcement that it "strongly encourages" businesses contracted with USAID to go beyond mandatory non-discrimination protections, to prohibit job bias for LGBT employees and other workers.

Among the top 10 countries granted economic and military assistance from the US, according to USAID, are Afghanistan, Iraq, Israel, Egypt Pakistan, Sudan, West Bank/Gaza, Ethiopia, Kenya and Columbia.