The students were exercising their constitutional rights and "should be praised for their idealism, not punished by being suspended from school," the NYCLU said in a letter sent last week.
Superintendent Craig Carr declined to comment, saying Thursday he hadn't received the letter.
Hundreds of students left Ralph G. Reed Middle School the morning of April 1, upset over proposed staffing cuts. The participants walked nearly a mile, picketing across from the early childhood center, which also houses the district's administrative offices.
Amol Sinha, director of NYCLU's Suffolk County chapter, said the punishment widens the disconnect between administrators and students, creating an atmosphere of hostility between the two.
The letter said the suspension "sends a message that free speech is unimportant and discourages future civic participation."
Sinha said he hopes the district will expunge the suspension from the students' records. He offered to meet with administrators to discuss the matter.
Autem Pike, an eighth-grader who helped organize the walkout through her Facebook page, was among those suspended.
She said she's proud of her participation but is also willing to accept the punishment.
"If any of us would have gotten hurt, I would have gotten the blame," she said.
But Pike's mother, Jennifer Cupid, said her daughter never should have been suspended. She said the school should have been more accommodating to the students.
"They should have called a meeting for the kids; take 15 minutes from their lunch or gym," Cupid said of school officials.
"They are always telling them to express themselves, but when they were ready to be heard, nobody was listening."