Emergency shelters were structures designed to provide refuge in the case of an emergency.
A number of these shelters were constructed by Starfleet in the 23rd century for use in drastic circumstances where housing large numbers of people was a priority. They were constructed of thermal concrete. (TOS: "The Devil in the Dark")
Starfleet ships had designated areas defined as emergency shelters which were more protected and could temporarily hold all of its crew in cases of emergency. The shelters of the USS Enterprise-D, for example, were used to conserve power from life support and auxiliary systems of non-shelter areas. All personnel were ordered to these areas during this time. (TNG: "Night Terrors")
In 2372, when a fleet of Klingon starships surrounded Deep Space 9, Constable Odo told Quark that he should be in an emergency shelter, but Quark insisted on staying in his bar to defend it. (DS9: "The Way of the Warrior")