UN Secretary General Ban accused many nations of the 54-member African Union of ignoring or "even sanctioning" discrimination based on sexual orientation or gender identity for "too long."
Outgoing African Union chairman Tedoro Obiang Nguema, who is president of Equatorial Guinea, speaking just before Ban delivered his speech, had accused "external powers" of perpetuating their influence.
South Africa is the only country on the continent that legally recognizes gay rights and same-sex marriage. Late last year, Uganda's parliament re-introduced a controversial bill that calls for the death penalty for certain homosexual acts.
Ban told summit leaders, whose two-day agenda is supposed to be focused on intra-Africa trade, that confronting homophobic discrimination was a "challenge."
"But, we must not give up on the ideas of the universal declaration of human rights," Ban said.
Tunisia returns to AU fold
Making an active return to the African Union is post-revolution Tunisia whose new president Moncef Marzouki said Tunis was looking to attract investors one year after its mass protests that triggered the so-called Arab Spring, also in Egypt and Libya.
Marzouki said ousted former ruler Ben Ali had not considered Tunisia as part of the continent. "Tunisia had no diplomatic role, especially in Africa. It (had) completely disappeared from the scene."
Tussle for AU leadership
AU leaders on Sunday elected Benin President Thomas Boni Yayi as their new president, to replace Equatorial Guinea's President Obiang.
Obiang, in his departing remarks, appeared to accuse former colonial powers of interfering. "Africa should not be questioned with regards to democracy, human rights, governance and transparency in public administration," he said.
Yayi, an economist who has led Benin for six years, acknowledged that he had a "high responsibility" in the one-year rotating job.
"We shall continue to work hand in glove to ensure that we consolidate all that we have achieved so far," he said.
The AU faces a string of issues, including war and hunger in Somalia, violence in Nigeria, riots in Senegal and oil disputes between Sudan and the newly formed South Sudan.
Ban highlights Sudanese oil dispute
UN chief Ban, in his speech, urged African leaders to play "a more important role [in] solving regional issues." He highlighted the Sudanese oil dispute and urged South Sudanese President Salva Kiir and Sudanese President Omar al-Bashir to negotiate.
South Sudan, which was born last July out of a peace deal, recently shut down oil production after it accused al-Bashir's Sudan of stealing oil along pipelines used for export.
Ban said he was also "deeply concerned" about a humanitarian crisis along Sudan's volatile border with the south. He also accused Khartoum of blocking access to aid workers.
Tussle for AU's top executive post
Monday's AU deliberations in the AU's new headquarter complex provided by China will center on a secret ballot for the top executive job. The current AU commission head Jean Ping of Gabon is being challenged by South Africa's Home Affairs Minister Nkosazana Dlamini-Zuma. Ping was first elected in 2008.
South Africa's foreign ministry said it was "optimistic" that Dlamini-Zuma, 62, and former wife of President Jacob Zuma, would receive the "necessary" two-third of the votes.
Dlamini-Zuma has the backing of the 15-member Southern African Development Community. Sources say Ping is counting on support of French-speaking AU member nations.
Ping told the opening ceremony that prospects for peace were "real" in war-torn Somalia. The AU has a 10,000-strong force protecting Somalia's fragile Western-backed government from the al Qaeda-linked Shebab militia.
Author: Ian P. Johnson (AFP, AP, dpa)
Editor: Nicole Goebel