The storms were within 34 miles (54.7 kilometers) and there were clouds within 8,000 feet (2,438 meters) of the landing strip at Kennedy Space Center, both violations of flight rules, NASA official said.
The shuttle has five more landing opportunities over the next three days. The next chance to land would be at 3:30 p.m. (1930 GMT).
"We're going to watch it a little bit and see how the next rev looks," Mission Control told Atlantis.
Mission Control said opportunities at Kennedy, the primary landing site, look slightly more promising on Friday and Saturday.
On Friday, they also could consider using a backup landing site in California. That backup site plus another in New Mexico would be activated Saturday if necessary.
Atlantis has enough power for its systems to orbit until Sunday, but managers want the shuttle to land by Saturday. The flight would only be extended to Sunday if there were technical problems that needed to be fixed.
NASA managers prefer landing at Kennedy since there would be less cost and time in preparing Atlantis for its next mission in December. It would cost $1.7 million (1.27 million EUR) and take up to 10 days to bring the shuttle back to Florida from California aboard a jumbo jet.
"Obviously, we would prefer to stay at the Cape if we can," said John Shannon, chairman of the mission management team.
Mission managers held an unusual, last-minute meeting Wednesday to clear up three remaining technical issues involving the shuttle. Material known as gap filler appeared to be sticking out of a wing, a thermal blanket had peeled back during the June 8 launch, and debris was found floating after Atlantis undocked from the international space station Tuesday.
Engineers had wanted to make sure the gap filler could withstand the heat and aerodynamics of re-entry and recheck data on the thermal blanket, which was repaired during a spacewalk last week. Mission managers have said the debris may have been ice.
During the crew's 13-day mission to the international space station, the astronauts installed a new truss segment, unfurled a new pair of power-generating solar arrays and activated a rotating joint that allows the new solar arrays to track the sun.
The mission was extended by two days to give astronauts time to repair the thermal blanket.
Atlantis commander Rick Sturckow said he was confident the repair job would hold up.
"Everything looks great," he said Wednesday in an interview with reporters.
The shuttle's visit to the space station was complicated by the crash of Russian computers that control orientation and oxygen production.
But the computers were revived several days later after cosmonauts Fyodor Yurchikhin and Oleg Kotov used a cable to bypass a circuit board. Astronauts conserved the shuttle's power in case they needed to spend an extra day at the station.
Sturckow got a haircut from Yurchikhin before leaving the space station. Astronaut Sunita "Suni" Williams said a haircut was one of many things she was looking forward to when she returns to Earth on the shuttle after more than six months at the station.
Williams set the record for longest single spaceflight by a woman.
"I'm looking forward to going to the beach and hopefully taking a walk with my husband and my dog on the beach," she said. "I can't wait for a good piece of pizza."