Sudanese voting in their first multiparty elections in 24 years on Sunday are expected to re-elect President Omar al-Bashir, who is accused of genocide in Darfur, in part because many of his opponents decided to boycott the vote claiming it had been rigged.

The elections, which are scheduled to be completed by Tuesday, are mandated by the Comprehensive Peace Agreement (CPA) of 2005 and are a step toward a referendum on southern independence scheduled for January.

But Mr. al-Bashir’s all-but-guaranteed re-election poses a significant challenge to the Obama administration, which is split on how to deal with the Sudanese leader, who is popular in Africa and neighboring Arab countries.

The U.S. envoy to Sudan, Scott Gration, has favored a policy of engagement with Mr. al-Bashir, but Susan Rice, the U.S. ambassador to the United Nations, has pushed for a more aggressive approach.

In the run-up to the elections, Mr. Gration spoke out in support of holding them on schedule despite opposition fears of a rigged vote, while Ms. Rice, who served as assistant secretary of state for African affairs in the Clinton administration, described the trends in Sudan as “very disturbing.”

Mr. Gration’s position more closely reflects that of President Obama.

Robert B. Lawrence, director of policy and government relations at the Save Darfur Coalition, described the U.S. commitment to the vote as “elections at any cost.”

“The U.S. approach is unfortunately short-sighted, because without true democratic reform of governance in Sudan, the ongoing challenges of economic and political marginalization in Darfur, South Sudan, and other regions will never be adequately addressed,” Mr. Lawrence said.

However, Sudan scholar Alex de Waal, program director at the Social Science Research Council, said, “It would have been preferable for a host of issues including the Darfur conflict, national reconciliation, restrictive laws, etc., to have been resolved before the election. But, in light of the CPA timetable and the consensus that the referendum should not be delayed, there are strong arguments for proceeding with these elections, in the knowledge that they will not be the last elections, and they will not obviate the need for attention to these other issues.”

Voting in Sudan on Sunday proceeded peacefully but was marred by confusion at polling places and logistical problems.

Former President Jimmy Carter, whose Carter Center is monitoring the vote, said that despite the snags, voting was proceeding smoothly.

“I believe the national election commission has done a good job, although there might be some slow delivery of material, but they have three days to correct that,” Mr. Carter said, according to Agence France-Presse.

The complicated elections require the electorate in the south to vote for a president for their autonomous region, as well as for a national president and parliament, state governors and legislators.

Groups monitoring the situation in Sudan cite a questionable 2008 census and voter registration process they say served the ruling National Congress Party’s interests, media censorship and oppressive security laws as reasons why a free and fair election is impossible.

The Brussels-based International Crisis Group has warned that an election under the present circumstances will have “catastrophic consequences” for Sudan.

Major opposition parties, including the Sudan People’s Liberation Movement (SPLM) and Umma Party, have boycotted the vote. Democratic Unionist Party (DUP) leader Mohamed Osman al-Merghani did an about-face on his boycott decision last week, which some Sudanese see as proof of a deal with the NCP to give legitimacy to the election.

Tiseke Kasambala at Human Rights Watch’s Africa division in Johannesburg said the boycott by the SPLM and Umma parties “points to an environment that is not conducive to free, fair and credible elections and does indeed raise concerns about the referendum and overall peace in the country if the situation is not addressed as a matter of urgency by the key actors in the country.”

Abel Alier, chairman of the National Elections Commission, insists his group has not favored Mr. al-Bashir’s party. “We are committed to free, fair polling,” Mr. Alier said, according to the Associated Press. “We want to ensure that what we do will make it evident both to the voter, to the ordinary citizen, and to the world at large that this process of polling is going to be transparent.”

The vote-rigging accusations raise the question of why Mr. al-Bashir, a popular leader among his people, would need to manipulate an election he is widely expected to win in the best of circumstances.

The International Criminal Court’s indictment against Mr. al-Bashir for war crimes in Darfur, while demonizing the Sudanese leader in the eyes of the West served only to lionize him as an anti-Western figure among African and neighboring Arab countries.