An analysis of images taken on Wednesday during lift-off in Cape Canaveral, in Florida, showed that the shuttle's underbelly was hit by a piece of ice, Shannon said.
"What this means, I don't know at this point," he said.
The possible damage was detected on Friday after ISS crew members photographed the shuttle's underside during its approach to the station.
On Sunday, astronauts are due to use a camera attached to a robotic arm to closely inspect the area of concern, Shannon said.
Astronauts will carry out a space walk to patch up the hole if Nasa decides the gash threatens Endeavour's safety during its return to Earth.
Shannon said that other shuttles have returned safely with worse damage.
"In the past, we didn't even know we had damage and we flew back home," he said.
But since the Columbia shuttle crash in February 2003, Nasa has carefully inspected protective thermal tiles.
Columbia's heat shield was pierced by a piece of insulating foam that from its external fuel tank, causing the shuttle to catch fire as it re-entered the Earth's atmosphere.
The shuttle exploded killing seven astronauts.