They were looking for the body of 46-year-old Eridania Rodriguez after a thorough search of her workplace yielded no clues.
Detectives "fear the worst," Police Commissioner Ray Kelly said.
"Right now we fear the worst. We did an extensive search of the building. We have sent detectives to a landfill in Pennsylvania. And we are talking to individuals in this case. We ask anyone with information of course to call our tips hotline, 1-800-577-TIPS."
Rodriguez was never seen leaving her workplace, and Kelly said the "investigative premise" is that something happened inside the office building, where she was a member of the cleaning crew.
"That's the theory that we are operating on, that something untoward happened to Mrs. Rodriguez inside the building."
Police were still searching basement floors of the skyscraper today.
They questioned two men who had access to the building, but neither was charged.
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