The ministry said in a statement late on Wednesday that the UN report includes "baseless allegations" that reflect "deep disregard" for Egypt's efforts to promote for human rights.
It also urged UN High Commissioner for Human Rights Zeid Ra'ad al-Hussein "to stop attacking the Egyptian state."
Egyptian President Abdel-Fattah el-Sissi is virtually certain to win another four-year term as he faces no serious challengers after a string of potential contenders withdrew under pressure or were arrested.