The incident happened when Mrs Clinton took the stage before an Institute of Scrap Recycling Industries meeting at the Mandalay Bay resort.
Mrs Clinton ducked and 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 du Soleil?" she quipped.
Many in the audience of more than 1,000 in a large ballroom laughed and applauded as Mrs Clinton resumed her speech.
"My goodness, I didn't know that solid waste management was so controversial," she said. "Thank goodness she didn't play softball like I did."
Brian Spellacy, US Secret Service supervisory special agent in Las Vegas, said the woman was being questioned and would face criminal charges. A black and orange shoe was recovered from the stage, he said.
Ilene Rosen, the wife of a delegate from Denver who was in the second row, said she saw an orange object fly towards the stage from a side aisle and papers fluttering in the air.
She 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 did not identify herself to reporters or explain the action. Security officials then ushered reporters and photographers away.
Mr Spellacy and Mark Carpenter, spokesman for the recycling institute, said the woman was not an accredited convention member and was not supposed to have been in the ballroom.
After her speech, Mrs Clinton answered questions posed by Jerry Simms, the outgoing chairman of the organisation. Mr Simms first offered what he called a "deepest apology for that crude interruption".
Mrs Clinton answered questions broadly, saying she felt politics today led 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 Defence document labelled confidential and dated August 1967, referring to an operation "Cynthia" in Bolivia.
Mrs Clinton has been travelling the US giving paid speeches to industry organisations and appearing before key Democratic Party constituents.
During a speech in San Francisco on Tuesday, she said she was seriously considering a presidential bid and all it would entail.