During a news conference Tuesday, Bedier called the incident a "deliberate act" targeting a congregation and pastor who have supported the local Muslim community on local and international issues.
"The writing's on the wall," Bedier said. "This was not some sort of random act."
The writing he referred to was "Traitors Support Terrorist" plastered in black marker on the wall.
The church's pastor thanked CAIR for speaking out against the vandalism, saying during the news conference, "Sometimes I feel that Muslims understand the message of Jesus better than we do."
The pastor had received hate mail after he appeared on the Bill O'Reilly Show in the past. O'Reilly called him out for supporting a drive to include Muslim holidays on the area school calendar.
Last April someone set fire to a Muslim school in the Tampa Bay area.
The following is from the St. Petersburg Times.
Vandals wreak havoc at church
Religious leaders say graffiti left on the wall constitute a hate crime
TAMPA - The Council on American-Islamic Relations and other religious leaders came to the defense of the Apostolic Catholic Church after the church was broken into Saturday. Graffiti that religious leaders called a "hate crime" was scrawled on the wall.
In the small Sulphur Springs church, the front door was broken down, a small amount of money was stolen, picture frames were broken and this message was left: "Traitors Support Terrorist."
A detective has been assigned to determine if the case falls under the state's hate crime classification, which would enhance the penalty if someone is found guilty of the vandalism, police spokeswoman Laura McElroy said.
The church's leader, Bishop Chuck Leigh, has been outspoken on several issues involving local Muslims.
He advocated the release of former University of South Florida professor Sami Al-Arian during the federal trial accusing him of terrorism ties.
Leigh also spoke in support of giving all religions school holidays during a contentious Hillsborough County School Board school calendar discussion.
The church is part of an independent Catholic movement not affiliated with the Roman Catholic Church.
"An attack on any house of worship is like an attack on all houses of worship, " said Ahmed Bedier, CAIR-Tampa's executive director, who urged anyone with information on the vandalism to contact police.
Church members fixed the damage and painted over the graffiti before Sunday's service.