But observers with the European Union and the Carter Center, led by former U.S. President Jimmy Carter, say the elections represented a key step toward democracy in Africa's largest country, the BBC reported.
Results are to be returned Tuesday, with Omar al-Bashir expected to be re-elected president after his two major rivals dropped out.
"It is obvious that the elections will fall short of international standards that are expected of advanced democracies," Carter said at a news conference. "The people's expectations have not been met."
Observers had reported seeing polling officials telling people which candidate to vote for and "harassment" of voters.
About 60 percent of the county's more than 16 million registered voters cast ballots for presidential, parliamentary and regional candidates in the elections, which resulted from a deal to end two decades of civil war.
The election has been marred by fraud accusations and logistical glitches. And several key parties and politicians opposed al-Bashir, who has ruled Sudan since 1989, boycotted the election over fraud concerns.
The vote had to be extended two days, to five, after the delayed arrival of electoral material led to the late opening of many polling stations, and observers also pointed to problems with the voting list.
Neither group called for a new vote, but said the observation provided lessons to be applied in next year's referendum on southern Sudan's independence.