The WESPAC Foundation, the group behind the ads, said they were meant to promote dialogue. However, City Council Member Lewis Fidler had a different view, the Daily News reported.
"This is a highly political campaign with a controversial underlying anti-Israel message," he wrote in a letter addressed to NY's Metropolitan Transportation Authority (MTA) President Thomas Prendergast." I would urge you to disallow and/or remove these advertisements."
However, activist Felice Gelman, a member of the group behind the ads, dismissed the charges.
"I have family in Israel. They deserve peace. And US policies are not helping," she said.
Meanwhile, pro-Israel group Stand With Us said it would post its own ads at NY subway stations later this month, the report said.
"We didn't ask for a billboard war," the group's CEO, Roz Rothstein, was quoted as saying. "But the group putting them up wants a response, and we have to give them a response."
The pro-Israel group's ad will show two boys with their arms over each other's shoulders. "The Palestinian Authority Must Accept The Jewish State & Teach Peace, Not Hate," the advertisement reads.
Only last month, the head of the House Foreign Affairs Committee asked Congress to block US funds for any United Nations entity that supports giving Palestine an elevated status at the UN.
Republican congresswoman Ileana Ros-Lehtinen was also seeking to ban US contributions to the UN Human Rights Council and an anti-racism conference seen as a platform for anti-Israel rhetoric.
AP contributed to the report