When you check in at the airport, which may be staffed by contractors not fully versed in EgyptAir policies, the check in agent will see the following information:
Information as of 11MAY15 / 1315 UTC
National India (IN) /Embarkation India (IN)
Transit Egypt (EG) /Destination Canada (CA)
ALSO CHECK DESTINATION INFORMATION BELOW
Egypt (EG)
TWOV (Transit Without Visa):
Visa required, except for Holders of onward tickets for a max.
time of 12 hours.
- Leaving the airport is permitted for passengers with transit
time between 6 and 12 hours. Passengers with transit time of
less than 6 hours may leave the transit area but not the
airport.
Therefore, I advise you obtain something in writing from EgyptAir confirming that your will be permitted on board the aircraft; failing that I would advise you to obtain the appropriate visa.
The check in agent will not violate what is said by TIMATIC unless they have a very good reason to do so, which could require a phone call from EgyptAir in Cairo.