Foreign ministry spokesperson Ahmed Hafez said on Wednesday he condemned "in the strongest terms" the call by the spokesperson for the UN High Commissioner for Human Rights, Rupert Colville, for an independent investigation into Morsi's death on Monday.
Hafez said it was a "deliberate attempt to politicise a case of natural death".
Egypt's first official comments on Morsi's death came amid growing criticism about prison conditions in the Middle East nation.
The UN human rights office said the investigation should encompass all aspects of Morsi's treatment during nearly six years of his incarceration.
Morsi was buried in a small family ceremony early on Tuesday a day after he suffered a fatal heart attack in a Cairo court, his sons said.
"Concerns have been raised regarding the conditions of Mr Morsi's detention, including access to adequate medical care, as well as sufficient access to his lawyers and family ...," Colville said in a statement.
"The investigation should be carried out by a judicial or other competent authority that is independent of the detaining authority and mandated to conduct prompt, impartial and effective investigations into the circumstances and causes of his death," he said.
Morsi was overthrown on July 3, 2013, after barely in power for a year in a coup staged by current President Abdel Fattah el-Sisi and placed under house arrest before being moved to prison.
Rights groups Amnesty International and Human Rights Watch have also called for a credible investigation into Morsi's death.
"The government of Egypt today bears responsibility for his death, given their failure to provide him with adequate medical care or basic prisoner rights," HRW said in a statement to Al Jazeera. "He's been in prison and treated worse than the already terrible conditions for Egypt's prisoners," Sarah Leah Whitson, executive director of the HRW's Middle East and North Africa division, told Al Jazeera, decrying Morsi's "terrible but entirely predictable" death."The Egyptian government has known very clearly about his declining medical state. He had lost a great deal of weight, he had fainted in court a number of times and was being kept in almost around-the-clock solitary confinement." A leading member of the Muslim Brotherhood group, Morsi won Egypt's first free presidential election in 2012, a year after an uprising that toppled longtime leader Hosni Mubarak.Turkey's ruling AK Party supported Morsi's government and many Brotherhood members and supporters have fled to Turkey since its activities were banned in Egypt in 2013."There are Arab dissidents and journalists who have been residing in Turkey since the Arab Spring began and people are here to give support for Morsi's cause," Al Jazeera's Sinem Koseoglu, reporting from Istanbul's Fatih Mosque, said.At the time of his death, Morsi, 67, faced a host of legal charges, which he, along with many human rights groups and independent observers, said were politically motivated.Thousands of members of now-outlawed Muslim Brotherhood organisation, who were arrested in the crackdown following the 2012 coup, are still languishing in jails.Egypt's government has dismissed accusations that the former president was badly treated.