As governments struggled to restore their economies, human rights were being "relegated to the back seat," Khan said.
She called for a "new global deal on human rights ... to defuse the human rights time bomb", and said governments must live up to their obligaions to uphold rights.
Sam Zarifi, the Asia Pacific programme director for Amnesty International in London, told Al Jazeera: "Unfortunately, over the last few decades there has been a tremendous lack of investment in providing human rights around the world and we are paying the price for it now.
"This is simply a recipe for disaster, especially as the world is now discussing pumping millions, billions and trillions of dollars into the economic infrastructure - it has to think about how it's going to build a better infrastructure that's more receptive to the people ... because after all, the economy is just an abstract notion for how well the people of the planet are living," he said.
The worst downturn in decades has plunged large parts of the world into recession, lowering industrial output and trade and rising levels of unemployment.
"The world needs a new global deal on human rights ... World leaders must invest in human rights as purposefully as they are investing in the economy"
Irene Khan, secretary-general of Amnesty
Protests against rising food prices and economic hardships last year were met with violent responses in many countries, and protesters were killed in Tunisia and Cameroon, Khan said.
Xenophobia was on the rise, she said, citing attacks on African immigrants in South Africa a year ago that killed at least 56 people.
"Billions of people are suffering from insecurity, injustice and indignity," Khan said.
"This crisis is about shortages of food, jobs, clean water, land and housing, and also about deprivation and discrimination, growing inequality, xenophobia and racism, violence and repression across the world."
World leaders were concentrating on attempts to revive the global economy but neglecting conflicts that spawned widespread human rights abuses, she said, citing Gaza, Sudan's Darfur region, Somalia, Democratic Republic of Congo and Afghanistan.
Hundreds of thousands of migrant workers had been laid off as export-driven economies slowed down, leaving more "disillusioned, angry, young men idle in their home villages and an easy prey to extremist politics and violence," she said.
Noting that nearly one billion people suffered from hunger or malnutrition, Khan said food shortages had been aggravated by discrimination and political manipulation of food distribution.
|Khas said the pending closure of Guantanamo prison is one "bright spot" [EPA]
In Zimbabwe, where five million people needed food aid by the end of 2008, the government used food as a weapon against its political opponents, she said, while in North Korea, the authorities deliberately restricted food aid to oppress people.
Wealthy countries were resorting to ever harsher methods to keep out migrants, she said. Some European Union states, such as Spain, had signed agreements with African countries to return migrants, or stop them leaving in the first place.
"Countries such as Mauritania see these agreements as a licence to arbitrarily arrest, detain in sub-standard conditions and deport without any legal remedy large numbers of foreigners on its territory," she said.
One positive factor in the outlook on human rights was a change in the US position on the war on terror, Khan told the Reuters news agency.
Soon after taking office in January, Barack Obama, the US president, ordered the closure of the Guantanamo prison camp for terrorism suspects.