The incident happened moments after Clinton took the stage before an Institute of Scrap Recycling Industries meeting at the Mandalay Bay resort.
Clinton ducked, and she did not appear to be hit by the object. She then joked about it.
"Is that somebody throwing something at me? Is that part of Cirque de Soleil?" Clinton quipped.
Many in the audience of more than 1,000 people in a large ballroom laughed and applauded as Clinton resumed her speech.
"My goodness, I didn't know that solid waste management was so controversial," Clinton said. "Thank goodness she didn't play softball like I did."
Brian Spellacy, U.S. Secret Service supervisory special agent in Las Vegas, said the woman was being questioned and would face criminal charges. Spellacy declined to identify the woman, and he said it wasn't immediately clear what the charges would be.
A black and orange shoe was recovered from the stage, Spellacy said.
Ilene Rosen, the wife of a conventioneer from Denver who was seated in the second row, said she saw an orange object fly toward the stage from a side aisle and papers fluttering in the air.
Rosen said the woman had walked down the aisle to within six rows of the front of the seating area, threw the items, turned around, put her hands in the air and walked toward the back of the room. Security officers quickly caught up with her.
In the hotel hallway, the middle-aged blonde woman sat calmly on a sofa, wearing a blue dress and thong sandals. She said she threw a shoe and dropped some papers, but didn't identify herself to reporters or explain the action. Security officials then ushered reporters and photographers away.
Spellacy and Mark Carpenter, spokesman for the recycling institute, said the woman wasn't a credentialed convention member and wasn't supposed to have been in the ballroom.
After her speech, Clinton answered questions posed by Jerry Simms, the outgoing chairman of the organization. Simms first offered what he called a "deepest apology for that crude interruption."
Clinton answered questions broadly, saying she felt politics today leads people to "do what they think will be rewarded."
An attendee later handed a reporter a piece of paper that was apparently thrown by the woman. It appeared to be a copy of a Department of Defense document labeled confidential and dated August 1967; it referred to an operation "Cynthia" in Bolivia.
The incident reminded some of former President George W. Bush dodging two shoes thrown by an Iraqi journalist during a news conference in Baghdad in December 2008. Shoe-throwing is considered an insult in Arab cultures.
Clinton, the former first lady and Democratic senator from New York, has been traveling the country giving paid speeches to industry organizations and appearing before key Democratic Party constituents.
During a speech in San Francisco on Tuesday, Clinton said she was seriously considering a presidential bid and all it would entail.