The naval vessels are the first from Iran to transit through the waterway since the country's 1979 Islamic revolution.
Last Modified: 22 Feb 2011 05:22 GMT
"They entered the canal at 5:45am," the official told Reuters news agency on Tuesday.
The two vessels, Alvand, a patrol frigate and Kharg, a supply ship, are the first naval vessels to go through the canal since Iran's 1979 Islamic revolution, after which diplomatic ties between Egypt and Iran were strained.
Egypt's ruling military council, facing its first diplomatic challenge since taking power on February 11, approved the vessels' passage through the canal.
The canal is a vital global trading route and a major source of revenue for the Egyptian authorities.
Israel takes a "grave view" of the passage of the ships.
On Sunday, after a weekly meeting of his cabinet, Binyamin Netanyahu , Israeli prime minister denounced the ships' arrival in the region as an Iranian power play.
And last week, the prospect of the Suez crossing was described by Avigdor Lieberman, Israel's far-right foreign minister, as a "provocation" by Iran.
But an Iranian diplomat said that, "This will be a routine visit, within international law, in line with the co-operation between Iran and Syria, who have strategic ties.
"The ships will spend a few days in Syrian ports for training purposes, having already visited several countries including Oman and Saudi Arabia," the diplomat added.
The decision was a difficult one for Egypt's interim government as Cairo is an ally of the United States and has a peace treaty with Israel.
However, Egypt's official MENA news agency has reported that the request for the ships to transit the canal was granted because they were not carrying weapons or nuclear and chemical materials.
The 1,500-tonne Alvand is normally armed with torpedoes and anti-ship missiles, while the larger 33,000-tonne Kharg has a crew of 250 and facilities for up to three helicopters, Iran's official Fars news agency said.