US President Barack Obama has called for gay rights in Africa during his landmark visit to Kenya, comparing homophobia to racial discrimination he had encountered in the United States.

In a joint press conference on Saturday after talks with Kenyan President Uhuru Kenyatta, Obama also pushed a tough message on Kenyan corruption, the civil war in South Sudan, controversial elections in Burundi and the fight against Somalia's Al-Qaeda-affiliated Shebab militants.

Obama arrived in Kenya on Friday, his first visit as president to his father's birthplace and the first to the East African nation by a serving US leader.

"I've been consistent all across Africa on this. When you start treating people differently, because they're different, that's the path whereby freedoms begin to erode. And bad things happen," he said after talks with the Kenyan leader, in response to a question on gay rights.

"As an African-American in the United States I am painfully aware of what happens when people are treated differently under the law. I am unequivocal on this," Obama told a joint news conference, openly disagreeing with Kenyatta.

He said that the notion "a law-abiding citizen... will be treated differently or abused because of who they love is wrong, full stop."

Homophobia is on the rise in Africa, and Kenyatta repeated the view that gay rights were "a non-issue."

"There are some things that we must admit we don't share. It's very difficult for us to impose on people that which they themselves do not accept. This is why I say for Kenyans today the issue of gay rights is really a non-issue," Kenyatta said.

A presidential visit to Kenya had been delayed while Kenyatta faced charges of crimes against humanity for his role in post-election violence seven years ago. The International Criminal Court has since dropped the case, citing a lack of evidence and accusing Kenya of bribing or intimidating witnesses.

President William Ruto, whose ICC trial continues, is also an unapologetic homophobe and has in the past described gays as "dirty".

Obama also had firm words for Kenya on civil rights and corruption, describing endemic graft as "the single biggest impediment to Kenya growing even faster," and saying people were being "consistently sapped by corruption at a high level and at a low level."

Obama said there was a need for "visible prosecutions," to show citizens action was being taken.