The archdiocese sent a subpoena to President Barack Obama's administration in February asking for documents from White House staff, including Obama himself, for use in a church lawsuit against the contraception mandate.
Citing the burden involved and calling a subpoena of the president's office inappropriate, the White House asked a federal judge to toss out the subpoena on April 4.
A notice filed in U.S. District Court in Washington late on Monday said the archdiocese agreed to withdraw its subpoena. It did not say why.
A lawyer for the archdiocese declined to comment on Tuesday. A spokeswoman for the U.S. Justice Department, which represented the White House in court, had no immediate comment.
The archdiocese is continuing its lawsuit in Brooklyn federal court challenging the Obama administration's health policy requirement that employers generally include coverage of birth control in health insurance plans they offer workers.
The Catholic Church teaches that artificial birth control is sinful because it violates natural law.
Part of the 2010 healthcare law championed by Obama and congressional Democrats, the birth control mandate has some exceptions for religious employers but the New York archdiocese said it expected to incur nearly $200 million each year in penalties if it refuses to comply.
(Reporting by David Ingram; editing by Andrew Hay)