Opponents of junta leader and presidential candidate Mahamat Idriss Deby Itno had called for a boycott, dismissing Monday's ballot as fixed.
And international rights groups had warned that the vote was not expected to be free or fair after a crackdown on the opposition.
On Sunday, four civil society associations, including the Chadian Human Rights League, hit out at the Deby-appointed electoral commission for refusing to accredit 2,900 of their representatives as voting observers.
"The EU in Chad condemns the non-accreditation of these civil society organizations," the EU said on Facebook.
"By so doing," the commission "blocked their contribution to the transparency of the electoral process financed by 3.8 million euros ($4.1 million) of European funds."
The head of the EU's political mission to Chad, Sona Jarosova, told AFP the bloc had "supported observation by Chadian citizens with EU funds."
General Deby on Tuesday hailed the vote as "a turning point in laying the roots of a culture of democracy in Chad."
The election came after three years of military rule in a country crucial to the fight against jihadism across Africa's Sahel desert region.
Deby's cousin and chief election rival Yaya Dillo Djerou was shot point-blank in the head in an army assault on February 28, according to his party.
Deby was proclaimed transitional president by army generals in 2021 after his father was killed in a gun battle with rebels following 30 years in power.
The International Federation for Human Rights on Friday said that the election appeared "neither credible, free nor democratic."
The International Crisis Group said "a number of problems in the run-up to the balloting cast doubt on its credibility."
These include measures allowing officials to publish only regional vote tallies rather than posting the results at individual polling stations — making it impossible for observers to verify the count.
Since the junta extended military rule in 2022, opposition figures have either fled, been silenced or joined forces with Deby.
Official results are expected on May 21.