Officials said 307 firefighters are now sidelined because of the illness.
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On Saturday morning, the department was 218 firefighters short so they had over 73 "priority 1" shifts being covered by firefighters working a second 24-hour shift in a row.
HFD was trying to replace those firefighters first. It's unclear how many replacements could be found.
"We have overtime money available for us," Houston Fire Chief Sam Pena told 13 Investigates. "It's just a matter of having the personnel available, the bodies to come to work."
Firefighter union president Marty Lancton sounded the alarm that the shortage could mean idled fire apparatus and delayed response times.
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"Depending on the staffing levels, you're either going to get a reduced response time for fire and EMS emergencies, or you're not going to have a unit that is closest to your house or your business," Lancton warned.
A fire tore through the office of Saint Francis Episcopal School on Piney Point near Westheimer around 10:30 p.m. Friday.
A Houston police helicopter spotted the fire from the sky. Upon arrival, one team cut holes in the roof while another climbed into the attic to put the flames out.
No injuries were reported. It was unknown what started the fire.
The firefighter union referenced the fire in a tweet later in the day Saturday, explaining, "The HFD command staff put Ladder 28, the busiest ladder truck in the city, out of service. The consequences? Late last night, Ladder 28 would have been first at the scene of the pictured fire on S. Piney Point Rd."
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As Pena's team scrambles to find firefighters to fill shifts, he called Saturday the "perfect storm." The July 4th holiday always brings extra calls. They will come on top of a 30% increase in calls for service in recent weeks.
The list of easy options is out of options.
"When you've sidelined that many personnel, it becomes difficult to staff units even in the best staffed departments," Pena said.
Both the department and union wanted to emphasize that 911 will remain open and firefighters will respond as best they can.