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It welcomed the government's resolution to research international methods of protecting the lesbian, gay, bisexual, transsexual and intersex (LGBTI) community, SAHRC spokesperson Isaac Mangena said in a statement.
Ugandan President Yoweri Museveni this week signed into law a bill allowing for repeat homosexual "offenders" to be jailed for life.
The legislation also outlaws the promotion of homosexuality and requires people to denounce gays and lesbians.
Mangena said: "The Commission believes that our government should make its rejection of Uganda's draconian law clear and visible.
"[We should] join those who respect the rights and freedoms of every person to call for the repeal of this and all similar legislation and to follow good human rights practices in line with its commitments under international and regional laws."
The SAHRC feared that the Ugandan law could endanger both Ugandan citizens and South Africans who work or travel in Uganga.
In 2011, South Africa introduced a resolution at the United Nations Human Rights Council (UNHRC) in support of gay rights.
Human rights
South Africa is a member of the UNHRC and was regarded as a champion of human rights.
"Our government, therefore, is rightfully expected and needs to speak out against all laws that seek to discriminate against and violate the rights of vulnerable and marginalised groups."
The SAHRC also rejected the notion that gay rights issues were a Western construct.
"The struggle for these and other freedoms has been at the heart of liberation struggles throughout the African continent.
"The South African government should actively engage with African countries that seek to outlaw fundamental freedoms and human rights, including gay rights, to desist from such intended practices," Mangena said.
Department of international relations spokesperson Clayson Monyela said in a statement on Tuesday that the government "takes note" of recent international developments regarding the LGBTI community.
"The government has decided to adopt measures aimed at significantly enhancing our protection mechanisms aimed at curbing violence against the LGBTI community," he said.
