In a letter addressed to the President, Schneiderman wrote that the National Security Entry-Exit Registration System, or NSEERS, created after the September 11, 2001, terror attacks, did not reduce terrorist activity and instead "undermined trust" in law enforcement and instilled fear in some communities.
"We can't risk giving President-elect Trump the tools to create an unconstitutional religious registry," Schneiderman said in a separate statement.
Last month, nearly 200 organizations concerned that the incoming president may revive NSEERS asked Obama to abolish the program before he leaves office
NSEERS, sometimes called "Special Registration," was a program for registering and monitoring noncitizen visa holders -- such as students, workers and tourists -- that President George W. Bush's administration enacted a year after the 9/11 attacks.
The program affected males 16 or older from 25 countries. With the exception of North Korea, all the countries on the list were Arab or had majority Muslim populations.
Proponents of NSEERS said it was necessary to identify and capture terrorists who might enter the country on false pretenses or who were already living in the United States.
Critics said it disproportionately targeted Arabs and Muslims, caused widespread fear within those communities and needlessly punished immigrants.
The program targeted men "regardless of whether they were suspected or accused of any wrongdoing," Schneiderman's statement said.
By 2011, nearly a decade after the program was enacted, NSEERS had not resulted in a single terrorism conviction. The Department of Homeland Security determined in 2011 that the program was "redundant and did not provide any increase in security," said Neema Hakim, a spokesman for the DHS. He said the program "has gone unused since then."
The Obama administration suspended the program by taking all 25 countries off its list, but left its primary structure intact.
That structure could serve as a blueprint for a future registry of Muslims nationwide, "creating an unacceptable temptation for future administrations to restart the program," according to Schneiderman.
Trump's transition team raised eyebrows last month when sources familiar with its plans said the President-elect planned to create a program similar to NSEERS. A source who spoke to CNN said the program Trump is considering would register and track foreign visitors from high-risk countries, including but not limited to Muslims.
CNN reached out to the Trump transition office for comment on the Schneiderman letter but did not receive a response.
Schneiderman has taken to Twitter to criticize the President-elect. On December 14 he tweeted, "I'm ready to stand-up and fight @realDonaldTrump, his dangerous appointees, and their radical agenda."
Schneiderman sued Trump in 2013, accusing his Trump University of fraud. Trump agreed last month to pay $25 million to settle three lawsuits, including the one filed by Schneiderman, against his namesake university.