Egypt's Alexandria and Dekheila ports, which both lie along the Mediterranean, were closed on Wednesday due to poor weather conditions, the Alexandria Port Authority said in a statement.
The ports are among the biggest in Egypt and each can handle a maximum of 1 million 20ft-equivalent units (TEUs).
High winds and a dust storm were blamed for the stranding on Tuesday morning of a 400-meter-long container ship that ran aground in Egypt's Suez Canal, blocking vessels from passing through.
Four Egyptian Red Sea ports had been shut on Tuesday, also due to weather conditions, and all except the Ain Sokhna port have now re-opened said the Red Sea Ports Authority and the Suez Canal Economic Zone Authority in separate statements.