UNICEF acknowledged progress by authorities in the country which has clamped down on the practice this year, but said the problem was still widespread.
"Egypt is one of the few countries in the Middle East where excision is a problem, with a level of 77 percent of young girls between 15 and 17 years and around 60 percent among girls under the age of three," said Ernon Manoncourt, UNICEF's representative in Egypt, quoting 2005 data.
The practice, which dates back to the pharaohs, was prevalent in "all classes, all level of society, urban and rural areas," she added.
Affecting both Muslim and Christian women, it was banned in Egypt in 1997 with doctors allowed only to operate "in exceptional cases". In June this year the government tightened the ban.
Manoncourt called for "pressure to be maintained so that the subject is not forgotten."
UNICEF calls the practice female genital mutilation and regards it as "one of the most persistent, pervasive and silently endured human rights violations."
Manoncourt said female circumcision was carried out by medical personnel in 75 percent of cases in Egypt, rather than by female elders at home.
An official said earlier this month that four Egyptian doctors and a midwife were to be prosecuted for conducting female circumcision following the death of two girls. Their private clinics were shut down.
A law to toughen penalties against the practice, prompted by the death of the two girls, is to due to be put to parliament's next session in November.