Masra, 40, a former opposition figure, is the main election rival of transitional president and junta leader Mahamat Idriss Deby Itno.
The election on Monday aimed to end three years of military rule but opponents of the junta chief called for a boycott, dismissing it as fixed.
Masra had ramped up considerable support on the stump in recent weeks and could force a second round of voting, scheduled for June 22.
Masra's party The Transformers said on Facebook that the 40-year-old economist was under "surveillance" and faces "threats to his safety."
The party and the political Justice and Equality Coalition which supports it also denounced "threats and serious violence" targeting their supporters as well as arbitrary arrests since Monday's vote.
The party complained that access to voting stations in order to observe the count had been denied.
And it said there had been "unimaginable violations, including shooting with live ammunition in order to monopolise ballots and reports of proceedings."
The Transformers urged people to "remain vigilant and mobilized to defend their will expressed at the ballot box."
EU says observers sidelined
Deby Itno was proclaimed transitional president by fellow army generals in 2021 after his father, Idriss Deby Itno, was killed in a gun battle with rebels following 30 years in power.
He promised an 18-month transition to democracy but then extended it by two years.
Opposition figures have since fled, been silenced or joined forces with Deby Itno.
His chief election rival and cousin Yaya Dillo Djerou was killed in February. His party said he was shot point-blank in the head in an army assault.
International rights groups had warned that the vote was not expected to be free or fair after a crackdown on the opposition.
Official results are expected on May 21.
The European Union on Tuesday criticized Chad's failure to allow nearly 3,000 civil society members financed by the EU to observe the presidential election.
"By so doing," the Deby-appointed electoral commission "blocked their contribution to the transparency of the electoral process financed by 3.8 million euros ($4.1 million) of European funds," the EU said on Facebook.
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