"The United States notes the initial assessment of independent electoral observers that Sudan’s elections did not meet international standards," he said.
"Political rights and freedoms were circumscribed throughout the electoral process, there were reports of intimidation and threats of violence in south Sudan.
"Ongoing conflict in (the western region of) Darfur did not permit an environment conducive to acceptable elections, and inadequacies in technical preparations for the vote resulted in serious irregularities," Gibbs added.
"The United States regrets that Sudan’s National Elections Commission did not do more to prevent and address such problems prior to voting."
State Department spokesman Philip Crowley also criticized the polls while calling them a "very important step" in implementing the CPA as it bolstered state governorships and assemblies that will oversee upcoming referenda.
Under the CPA, the Sudanese are set to hold a referendum in January on whether the mainly Christian and animists in the south will remain part of Sudan, which is dominated by the majority Arabs and Muslims in the north.
They are also set to hold a referendum next year on the status of the contested oil-rich region of Abyei.
He expressed less concern with the wide expectation that Omar al-Beshir -- who faces an international warrant for arrest on charges of war crimes in the Darfur -- is likely to win yet another term as president.
Crowley, the assistant secretary of state for public affairs, said the United States would continue to work with the central government in the north and the semi-autonomous government in the south.
In Khartoum, Beshir's ruling National Congress Party rejected the US accusations that the landmark polls were not free and fair, but welcomed the offer for cooperation.
In Washington, the Save Darfur Coalition, a group defending the rights of the people in Sudan's western conflict-torn region of Darfur, criticized the Obama administration for being too soft on Khartoum.
"We were pleased to see that they (the Department of State) were honest in their assessment," Robert Lawrence, Save Darfur's political director, said after the United States had taken a low profile during the campaign.
While the group understood the need for Washington to play the role of "honest broker" and promote "dialogue between all parties," it is bothered that Washington "doesn't really assign responsibilities to the problems," he said.
"We would like to see a more balanced engagement policy that takes into account the fact that the NCP has broken so many promises over the years."
Enough Project, another group that observes Sudan closely, late Monday posted a video on YouTube showing alleged ballot stuffing at a Sudanese voting booth.
John Prendergast, a co-founder of Enough, said the Obama administration, in validating an electoral process while also recognizing major shortcomings, "believes it is simply moving the ball forward in pragmatic fashion inexorably toward the referendum.
"Rather, the administration is sending yet another signal to the Sudanese parties that there will be no repercussions for significant violations of the North-South peace deal," he said in an email exchange with AFP.
"This puts at greater risk the necessary preparations for the referendum, the implementation of the remaining elements of the North-South peace deal, and the possibility of successful negotiations in Darfur."
"The stakes continue to get higher, and the administration's bar for moving forward continues to get lower," Prendergast added.