Pelham Public Schools administrator Cheryl Champ wrote to employees telling them the banner was outlawed, claiming it "has increasingly been perceived by students to be threatening in nature", causing them to feel "unsafe".
The sweatshirt was created by the daughter of late Transit Police Detective George Caccavale, who was fatally shot in 1976. She sold the designs to raise funds for police foundations after a K-9 dog was named Vale in tribute to her deceased father.
But after a number of Pelham school officials ordered the sweatshirts Champ sent an email to say they, and face masks with the thin blue line patch, were banned. There was no mention in her first email of a prohibition focusing on any other changes.
Designer Carla Caccavale, 44, told her "is not into politics at all", continuing: "This was never about politics. It was about honoring my father."
Caccavale, who was just 20 days old when her father died at age 33 working a second job at a check-cashing store, added: "This is not Black Lives Matter versus police. This was never the intent when we created the sweatshirt."
After her original email in October Champ then told staff in another letter on November 3: "I recognize that in these heightened political times, these decisions, which were made on a case-by-case basis, have become intertwined and perceived by some to reflect a political leaning on behalf of myself and the district.
"Like many symbols whose meaning has been co-opted over time, the thin blue line flag has increasingly been perceived by students to be threatening in nature, causing them to feel unsafe within our schools.'
After the president of the NYPD's detectives union, Paul DiGiacomo, took issue with the ban Champ appeared to change her stance.
She wrote: "Decisions made last week did not evenly support our ideals of political neutrality."
Champ then said teachers should not wear any clothes that can be regarded as political, including care for "and social movements such as those represented in our schools last week on T-shirts and masks."
Students are not involved in the prohibition.
The schools district told: "This was specifically about disallowing staff attire displaying symbols considered to have political meaning, including, but not limited to the blue line flag." But Caccavale added: "The issue is still that a blue line flag is not political."