Former Malian president and head of the AU observer mission to Chad, Diouncounda Traore, said issues included the late opening of polling stations in hard-to-access areas and poorly trained polling officers.
He said he doesn’t know what will happen after the proclamation of the results, but the AU is urging all candidates and their followers to accept the verdict. He said those who are not satisfied with the results should contest them in the courts.
Kamalloh Salifou Tourabi, leader of the Pan African Institute for Election Assistance observer mission, said that despite irregularities, voter participation was estimated at 85 percent.
The opposition said there was fraud, including ballot stuffing.
Chadian president Idris Deby is widely expected to win a fifth term in office.
The country faces continued threats from the Nigerian terror group Boko Haram. Social issues like the high cost of living sparked unprecedented protests in the run up to the poll. Five rights activists have been in jail for the last three weeks.
Chad has cracked down on the media, in particular the foreign press, since the vote. The French broadcaster, TV5 Monde, said its crew was forbidden from filming.
Mahamat Abdoulaye Issa, Chad's official in charge of press accreditation, said journalists were not authorized to report as the country waits for results.
Issa said journalists wishing to report on non-election related issues must apply for new accreditation to remain in Chad. He said that does not infringe on press freedom.
The electoral commission has two weeks from the April 10 vote to declare results.