The strategic waterway is one of the main sources of foreign currency, bringing around $5 billion a year at a time when the country faces political unrest and economic turmoil.
The new toll fees will start after midnight on Tuesday, an official from the Suez Canal Authority said. They will rise 5 percent on oil tankers and petrochemical products and 2 percent for container ships and car carriers.
Last year, tolls were raised by 3 percent for all ships passing through the canal.
The 192-km (120 mile) canal is the quickest sea route between Asia and Europe, saving an estimated 15 days of journey time on average. (Reporting by Asma Alsharif; Editing by Louise Heavens)