Temperatures are expected to drop in the Greater Cairo area, the Nile Delta, South Sinai, and northern Upper Egypt, the EMA said in its bulletin on Tuesday.
The North Coast from Alexandria to Matrouh will see nippy weather and strong winds, it added.
The Greater Cairo area and the Nile Delta are expected to see highs of 21-22 degrees Celsius and lows of 11-13 degrees Celsius.
The North Coast will see highs of 18-19 degrees and lows of 12-13 degrees.
Highs in South Sinai will drop from 30 degrees on Wednesday to 25 degrees on Friday, while lows will range between 16 to 14 degrees.
In Luxor and Aswan in the deep south of the country, highs will drop from 33 degrees on Wednesday to 27 degrees on Friday. Lows will hover around 15-16 degrees.
Minya and Beni Suef in northern Upper Egypt will see highs drop from 27 degrees to 22 degrees, and lows will be around 11.
The EMA also predicts a 30 percent chance of mild rainfall and strong winds on Wednesday and Thursday on different parts of the North Coast and the northern parts of the Delta.
The EMA also warned of disruption in maritime navigation on Wednesday, Thursday and Friday along the Mediterranean Sea and the Gulf of Suez.
Wind speed along the Mediterranean will range between 50 and 70 km/h and the height of the waves will range between 3 and 4 metres.
Meanwhile, wind speed along the Gulf of Suez will hover at 40-70 km/h and the height of the waves will hover at 3-5 metres.
Warmer temperatures will return for much of the country on Saturday.
On Monday, highs in the Greater Cairo area, Nile Delta and South Sinai could reach 29. The North Coast will see 27 and Upper Egypt 30.