A Brentwood student going to school on Wednesday was approached by “a few individuals in a red car” who took his light blue T-shirt, set it on fire and warned him not to wear that color — prompting an immediate warning to parents in an area reeling from a spate of killings linked to gang violence.

Schools superintendent Levi McIntyre on Wednesday issued a letter and placed a robocall, asking parents and guardians in Brentwood to watch what their children wear to school.

“Please know that school officials will continue to remind students to be observant of their surroundings and report any suspicious activities immediately,” said McIntyre’s letter, posted on the district’s website. “We are also asking parents to be vigilant in monitoring their children and be aware of their location at all times. We also ask that children not wear clothing that could be considered to be gang-affiliated.”

Gangs are known to adopt insignia and colors to identify their members, and their enemies, in street turf wars.

In the robocall to parents of children in the high school, McIntyre referred “more specifically to be observant of the color clothing they wear so they don’t attract negative attention,” district spokesman Felix Adeyeye said Thursday, but he didn’t specify what colors to avoid. The incident has been reported to Suffolk police, who are investigating, he said.

The warning left some residents perplexed and angry.

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“It’s disgusting that kids are doing this,” said Susan Baker, a parent advocate. “I really don’t know how people should respond. You can’t really avoid all these colors… Now, parents are scared to send their kids, and that shouldn’t be.”

The threat to the unidentified ninth-grader attending the district’s Freshman Center came after the beating deaths last week of two girls, both students at Brentwood High School’s Ross Center, and the discovery of two sets of human remains in a wooded area in Brentwood.

Sources familiar with the investigation say that FBI agents and federal prosecutors believe those cases may be connected to an extremely violent group of MS-13 gang members.

According to McIntyre’s letter, the student threatened was “walking to the bus stop” in an undisclosed part of Brentwood when the driver of the vehicle “demanded the blue shirt” he was carrying in his hand.

The shirt was torched and thrown out the car window.

“The student was told not [to] wear that color again,” McIntyre wrote.

Blue and white have been associated with the MS-13 gang, which originated in Los Angeles and has spread to Central America and other U.S. metro areas, according to a law enforcement gang-awareness guide. The MS in the name stands for the words “Mara Salvatrucha” — slang for Salvadoran gang — and those colors match the ones found in the flag of that country.

Other gangs identify with colors such as blue, red and golden or yellow, the law-enforcement sources said.

The warning leaves parents and students with little recourse, said a community advocate from neighboring Central Islip.

“What parents know what colors they should keep their kids from wearing?” said Renee Ortiz, who will be moderating a community forum next week in response to the recent killings. “Yesterday was blue, tomorrow is red and next is yellow? Will there ever be a color that is OK? We have to work to attack this at the root instead of remaining forever a reactive community.”

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More resources are needed so that Brentwood and surrounding areas receive better policing, children have more alternatives and teens are rescued from gangs, Ortiz said.

Adeyeye said the district, which educates about 1,100 ninth graders and has about 4,700 students in grades 10 through 12, has upgraded security measures, randomly putting entire classes through metal detectors and requiring staff and students wear visible identification cards while on school premises.

Wednesday’s incident, he said, took place away from school and beyond the reach of school security staff.

Adeyeye said there was no notable change in attendance at Brentwood schools on Thursday, as did an administrator in neighboring Central Islip schools.