Governor Wanda Vazquez said the goods had sat unused since the September 2017 disaster, which killed an estimated 3,000 people.
She ordered an investigation and described the inaction of Carlos Acevedo, the director of the office of emergency management (NMEAD), as “unacceptable”.
“There are thousands of people who have made sacrifices to help those in the south, and it is unforgivable that resources were kept in the warehouse,” the governor said.
Ms Vazquez nominated Jose Reyes, who oversees the National Guard in Puerto Rico, as the new commissioner for the agency.
A group of angry citizens broke into the warehouse in the southern coastal city of Ponce before the governor made the announcement.
Hours before his dismissal, Mr Acevedo had rejected claims that supplies were being wasted after a video showed thousands of bottles of water stacked in the warehouse.
“The citizen who entered today to share the images on social networks, violated the security perimeter, which represented a risk for him,” he said in a statement.
“For this reason, our colleagues instructed him to leave the area.”
The US territory is still recovering from 6.4 magnitude earthquake earlier this month which left one person dead and caused an estimated $200m (£154m) in damage.
More than 7,000 people remain in shelters since the quake, which is said to have been the biggest to hit the island in a century.
Additional reporting by Associated Press