In the Human Rights Council's first review of Egypt's rights record since 2010, which covers the period since long-ruling leader Hosni Mubarak was toppled to the turbulent ousting of Morsi, several Western envoys voiced alarm at the worsening human rights situation in Egypt.
Rights groups including Amnesty International and Human Rights Watch said the situation is unprecedented and urged the council to order an international probe into the crackdown, mass arrests and unfair trials.
But Egypt hit back, insisting that the government of Abdel Fattah al-Sisi had made human rights a priority since toppling Morsi in June last year.
"The prioritisation of human rights is at the core of the political life of the new administration," Egyptian Minister of Transitional Justice Ibrahim el-Heneidy told the council.
"Egypt will fulfil its international obligations," he said.
But Western diplomats voiced doubts.
US envoy Keith Harper cited in particular the government's crackdown on Morsi suppporters in July and August 2013 that "resulted in a large number of deaths of Egyptian citizens".
"We are concerned about the lack of accountability for those accused of human rights abuses" in these incidents, he told the council.
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Sisi's government began clamping down on Morsi supporters after the Islamist president was ousted in July 2013, leaving at least 1,400 dead and more than 15,000 jailed. Hundreds have also been sentenced to death after often speedy trials.
Over a period of just a few days of clashes in Cairo in August 2013, police killed hundreds of protesters.
Britain's Karen Pierce raised concern over "the numbers of detainees in pre-trial detention, reports of mistreatment or torture, use of mass trials and trial irregularities (and) retention of the death penalty."
She also decried the decreasing space for civil society and the media to operate."
Sweden's representative meanwhile highlighted "the precarious situation of women in Egypt," calling for legislative reform to "combat sexual harassment and gender-based violence."
Seven Egyptian non-governmental organisations announced Wednesday that they would not participate in the UN's Universal Periodic Review, which all 193 UN countries must undergo every four years, for fear of reprisal.
Cairo has set a November 10 deadline for all NGOs to register with the government, in a move activists warn will deal a death blow to the country's civil society.
"Civil society is on the verge of disappearing," warned Philippe Dam of Human Rights Watch.
Nicholas Piachaud of Amnesty warned via video link that many people in Egypt were facing "grossly unfair trials", while others were disappearing and "torture is once again rife."
"All of these things are happening against the backdrop of rampant discrimination," he said, demanding "robust action" from the council.