They are telling riders they don't have to go along with the new program, arguing it violates a person's constitutional right against an unreasonable search.
"No American should have to prove his innocence in order to walk the streets or ride on public transportation," said Steven Silverman, executive director of the Flex Your Rights Foundation.
Metro says the program, announced Monday, is designed to prevent a terrorist attack and improve overall safety within stations.
"And what people need to understand is our job is to protect the riding public and Metro employees from any sort of harm," said Metro Transit Police Deputy Chief Mark Olson.
Metro says this initiative is modeled after New York City's program, which has survived a court challenge.
But Mark Rotenberg with the electronic privacy information center says recent research indicates some of these programs aren't effective.
"Increasingly the government is pursuing programs that look effective and make people feel better but there's no real opportunity to evaluate the program and decide if in fact it's working," he said.
Metro's decision has many riders talking.
"I would probably refuse. I think it's ridiculous," said Janyne Quarm, a Metro rider. "It's going to slow down Metro.
While some riders say getting a bag searched could be time consuming and bothersome, most riders are not troubled by this latest security measure.
"I guess it's not a big deal to me," said Mike Hoehn. "I don't have anything to hide."
Metro says if riders refuse to have a bag searched -- which they have the right to do -- they will be asked to leave the station. They can return and ride as long as they don't bring back the bag.
Metro has not announced exactly when the program will begin.
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