Thunderstorms packing heavy rains and lightning have caused widespread flooding across Egypt, killing at least five people and injuring five others, officials have said, as authorities shuttered schools, government offices and an airport.

Thursday was declared a paid holiday to keep streets clear, closing schools and government offices, with officials urging people to stay at home and not to park near trees or in low-lying areas that would be at risk of flooding.

A driver died when strong winds blew his car into a canal in the southern province of Sohag, and a technician was electrocuted in New Valley province while trying to repair a lighting column that had lost power due to the heavy rain.

A child and five people were wounded when floods demolished their houses in a rural area in the southern province of Qena. Lightning also ignited several fires.

A state of emergency began on Wednesday as a powerful storm developed over the Mediterranean Sea, prompting authorities to issue warnings to residents.

On Thursday, authorities closed down the Luxor International Airport, a key hub for tourists, as well as the Mediterranean port of Alexandria and the Red Sea port of Sharm el-Sheikh.

The city of Ismailia, situated on the west bank of the Suez Canal, recorded 25 millimetres of rain in 24 hours. Mersa Matruh, a resort town on the country's Mediterranean coast, reported 20mm.

Despite such relatively small rainfall totals, many parts of the capital, Cairo, were underwater.

Chaos generally accompanies bad weather in Egypt, raising questions about the country's poor infrastructure and dilapidated sewage and drainage systems.

Late on Thursday, Cairo's Water Authority announced it had suspended water service to the entire city because heavy rain had overwhelmed the vast sewage system. It said water would return when the weather improved, without offering an exact time.

Mahmoud Shahin, director of the analysis department at the Egyptian Meteorological Authority, said: "This level of instability in weather conditions has not occurred with such force since 1994."

Egypt has no comprehensive rainwater drainage system and relies on a 105-year-old drainage network to siphon rainwater.

In an earlier statement on the floods that brought Cairo to a standstill last October, the cabinet said that Egyptian cities were built without rainwater drainage networks.