Both women claim to have been attacked by Blaine in separate incidents more than 20 years ago in Manhattan.
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At least one of the incidents appears to fall outside the statute of limitations.
Chief of Detectives Dermot Shea confirmed Monday at an unrelated news conference that Blaine is under investigation, but he declined to discuss any details.
"We are aware of the allegations," he said. "There's an active special victims investigation."
Shea did not discuss specifics or state when the investigation began.
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Blaine has not been charged, nor has he been interviewed.
"The NYPD takes sexual assault and rape cases extremely seriously and urges anyone who has been a victim to file a report so we can perform a comprehensive investigation and offer support and services to survivors," the NYPD said in a statement.
Blaine denies the allegations and intends to cooperate with authorities, his publicist said in a statement Tuesday.
"David denies the accusations that have been reported and he takes these allegations seriously," the statement from Blaine's publicist said. "He intends to cooperate with any investigation."
Blaine, 45, is known for stunts like being buried underground for a week without food or water in New York in 1999. He also lived in a plexiglass case suspended 30 feet above the Thames River in London for more than 40 days in 2003.
He is scheduled to start a tour of the United Kingdom and Ireland in June, according to his website.
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