The UN called for an investigation on Tuesday after Morsi collapsed and died during a court appearance this week.
In a statement, Egyptian Foreign Ministry spokesman Ahmed Hafez "condemned" the suggestion, insisting it was "a case of natural death", the BBC reported.
Egypt's comments on Morsi's death came amid growing criticism about prison conditions in the country.
Morsi had been in custody since his removal in a 2013 military coup. His family have long raised concerns over his treatment in prison and say that the authorities refused a request to bury him in his home town.
The former leader was instead laid to rest in eastern Cairo early on Tuesday, reportedly under tight security.
Hafez accused the UN of trying to "(obscure) the institutions of the Egyptian state and the integrity of the Egyptian judiciary". He added that any suggestion of foul play was "not based on any evidence".
A statement earlier this week from the office of the UN High Commissioner for Human Rights pointed to Egypt's obligations to treat its prisoners humanely.
"Concerns have been raised regarding the conditions of Morsi's detention, including access to adequate medical care as well as sufficient access to his lawyers and family during his nearly six years in custody," a spokesman for the office said.
"He also appears to have been held in prolonged solitary confinement."
Morsi died while appearing in court on spying charges. He was already facing decades in jail after being convicted in previous trials on separate charges.
A forensic report has been ordered into his death.
His former party the now-banned Muslim Brotherhood and Turkish President Recep Tayyip Erdogan, a close ally of Morsi, are among those who have blamed the Egyptian leadership for his death.
Human rights groups including Amnesty International and Human Rights Watch also called for an independent investigation into Morsi's death.
( With inputs from IANS )