The shuttle, perched at an oceanside launchpad, is wrapped in a protective metal structure but much of its fuel tank and twin solid rocket motors are open to the elements.
Mixed in with the rain were chunks of ice that hit exposed parts of the shuttle.
Nasa technicians planned to move the orbiter back to a giant hangar to examine the damage and decide if repairs can be made at the Kennedy Space Centre.
"This constitutes, in our evaluation, the worst damage we have ever seen of hail on the external tank," Wayne Hale, manager of the space shuttle programme, said on Tuesday.
The 11-day mission for Atlantis includes delivering a 15,875-kg addition to the International Space Station, the heaviest ever.
The astronauts are also supposed to conduct at least three spacewalks.