Officials later said a false sensor reading or computer problem likely set off the alarm, rather than an actual leak of ammonia coolant.
"No signs of a leak," NASA said via Twitter. "Controllers are assessing."
In the meantime, the six crew members huddled safely on the Russian side of the orbiting outpost, as Mission Control analyzed the data through the morning.
"Hey everybody, thanks for your concern," Italian astronaut Samantha Cristoforetti said in a tweet. "We're all safe & doing well in the Russian segment."
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As alarms blared, the astronauts followed emergency procedures in turning off non-essential US equipment, taking cover in the Russian quarters, then sealing the hatches between the US and Russian sides.
NASA said because of the possibility of leaking liquid ammonia it's used to cool electronics the entire crew was ordered over to the Russian side. The three Russians, two Americans and the Italian Cristoforetti will remain there until further orders; mission managers gathered in Houston at midmorning to discuss the situation.
There's enough food and supplies in the three Russian segments for all six to stay there a week, although that isn't anticipated given that there doesn't appear to be a leak.
Commander Butch Wilmore, an American, and his crew were busy dealing with supplies from the newly arrived SpaceX capsule when the ammonia-system alarm sounded.
The 260-mile-high complex has never had to be abandoned during its 14-year-plus occupation by astronauts. On occasion, crews have had to seek shelter in their Soyuz capsule "lifeboats" because of close shaves with orbiting junk, in case a quick getaway was needed. This time, the astronauts went into one of the three Russian modules, but not the two docked Soyuz capsules.