The Harris County Sheriff's Office responded to a criminal mischief call at 1800 Baker Road after an employee spotted the damage.
Hesham Ebaid is the vice president of the center. He said if the shots were fired any other hour of the day, they could have led to injuries.
"Luckily enough, it was 3 o'clock in the morning, so nobody was here," Ebaid said. "Thanks to God, we have no injuries."
One bullet hit the front of the building. The other struck a vehicle in the parking lot.
Ebaid said they hope the gunman is caught, but they're eager to forgive him.
"I think he is misinformed about who we are and what we do as a Muslim in this country," Ebaid said. "We are citizens in this country. We are a good working people here. We pay taxes. We are a part of this country."
The center is working to increase security measures after the incident.
They're also working with Harris County investigators and have also been in contact with the FBI. However, they're not ready to assume this is hate related until the investigation is complete.
"This such event will not stop us from coming to our worship place," Ebaid said.
The Houston chapter of the Council on American-Islamic Relations (CAIR-Houston) is encouraging a thorough investigation of Tuesday's incident.
As one of the nation's largest Muslim civil rights and advocacy organizations, CAIR-Houston is also seeking donations for the mosque and the Houston Quran Academy to aid in increasing security efforts on the property.
"We are relieved that no one was harmed in this attack," Arsalan Safiullah, CAIR-Houston Civil Rights Attorney said. "But we are deeply disturbed by the unprecedented spike in attacks and threats targeting houses of worship nationwide."
Crime Stoppers will pay up to $5,000 for information leading to the the identity of the suspect. Information may be reported by calling 713-222-TIPS (8477) or submitted online at www.Crime-Stoppers.org.
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