Clooney, an actor and film director but also a long-time human rights activist, met with Obama and later with Senate Foreign Relations Committee Chairman John Kerry, D-Mass., and Sen. Richard Lugar, R-Ind., the top Republican on the committee, to call for diplomatic actions directed at Sudan "before people start dying."
Southern Sudan, a quasi-autonomous state with a population of about 8 million people, will decide Jan. 9 whether to become independent or to remain part of the Government of National Unity created in 2005 after more than two decades of civil war.
Clooney, who recently visited Southern Sudan with John Prendergast, the founder of the anti-genocide group Enough Project, and NBC News' Ann Curry, said that the referendum may drag the country into another spiral of violence.
"We have about 90 days before will be facing a real disaster," Clooney said.
Lugar also urged Congress to "take seriously what's happening in Sudan."
Clooney said that all the people he met during his trip seemed to be determined to gain independence, which might cause a violent reaction from the north.
"We know the players involved," he said. "They are the same people who were involved in Darfur."
In 2009, U.S. Secretary of State Hillary Clinton announced that one of the key goals of the Obama administration in Sudan was to guarantee a peaceful post-referendum situation.
Since 1953, when Sudan, the largest African country, became independent from the United Kingdom and Egypt, the Muslim-dominated north and the south have engaged in two civil wars. While rooted in religious and ethnic differences, these conflicts were also caused by disputes over the control of economic resources, namely oil.
The first civil unrest broke out in the 1950s and ended in the early 1970s. The second, started in 1983, ended only in 2005 after the signing of a peace agreement and left more than 2 million people dead, according to the Department of State.
A report by Human Rights Watch found that the humanitarian situation in southern Sudan was still precarious in 2009. In the absence of a functioning rule of law system, civilians, according to the report, are often attacked by soldiers and other security forces.
Although the Department of State still lists Sudan as one of the states that sponsors international terrorism, since 2005 the United States has invested in the country more than $8 billion in humanitarian aid.
"We already involved," Clooney said. "If we do it now, it doesn't cost us any money."