Vacuuming trucks were deployed to the tunnel to extract the water, the source said, adding the tunnel was reopened after an hour of closure.
The tunnel is the longest in Cairo, 2.6km long, and one of its most important, carrying thousands of cars every day.
In March, the head of the Azhar Tunnel Operation Authority, Ibrahim Samaha, announced his resignation, saying that there had been several technical issues in the tunnel and that requests to fix them had been ignored.
He also told the media that he couldn’t afford to wait any longer; he feared a catastrophe in the tunnel and, as head of its authority, he would be blamed.