A woke Long Island teacher was forced to remove two Pride flags from her classroom after students complained that one of them made them “uncomfortable” — prompting Gov. Kathy Hochul to launch an investigation.

The flag flap erupted when Sarah Ecke, a math teacher at Connetquot High School in Bohemia, refused to take down a Rainbow flag and a Progress Pride flag, Newsday reported.

Some of the students had complained that the Progress flag — which has more colors than the traditional version — left them “feeling uncomfortable,” according to the news outlet.

The Suffolk County district notified parents that the teacher was told several times to remove the Progress flag but was allowed to continue displaying the traditional one, News 12 reported.

But last week, the district issued a directive banning all flags except the US and state flags, citing its policy that employees should not engage in political activities in school.  

Ecke, the adviser of the school’s Gay-Straight Alliance club, has removed the flags after principal Michael Moran warned her in a letter that she could face disciplinary action for failing to comply, David Kilmnick, president and CEO of the LGBT Network, told Newsday.

LGBTQ advocates accused the district of violating the state’s Dignity for All Students Act by ordering the flags removed, prompting Kilmnick to call on Hochul and state education chief Betty Rosa to investigate “Connetquot’s deliberate, intentional and discriminatory actions.”

“Governor Hochul is committed to protecting the human rights of New Yorkers, and has directed the Division of Human Rights to investigate potential violations of Human Rights Law in this matter, consistent with the agency’s mandate,” Hochul’s office told the paper in a statement.

Connetquot Schools Superintendent Lynda Adams has previously said Ecke was told to remove the Progress flag and keep the traditional one as a “compromise” that she rejected along with a district offer of a sign that reads: “This is a safe space to be who you are.”

“Unfortunately, with this continued refusal, the district must now fully implement Policy 1310 which states that school employees shall not engage in political activities on school premises,” the schools chief reportedly wrote.

“By adhering to the letter of the Policy, we can neutralize the environment, hopefully making the space feel safe and comfortable for all of our students,” Adams added.

In a response to a request for comment by The Post, the district provided a statement it had shared at a school board meeting Tuesday.

“Please be assured, it was never the district’s intention to create a perception that our schools are not safe and welcoming spaces for all,” the district said. “In fact, our work to implement alternative solutions is proof of the opposite.”

It added: “Each of our children deserve a school where they are safe, comfortable and respected, regardless of what race, gender, religion, sexual orientation, or political affiliation they espouse to and we look forward to continuing to support one another as such.”   

Meanwhile, a rally was held Tuesday outside Oakdale-Bohemia Middle School, where some people were draped in Rainbow flags.

Helen Werner, 21, a 2021 Connetquot High grad, said her fear of being bullied prevented her from coming out in high school.

“I’m trans and I’m bisexual, and I did not feel comfortable coming out in Connetquot,” she told Newsday Tuesday night while about 30 counter-protesters waving American flags congregated nearby.