The Justice Department said Wednesday that it was suing Uber Technologies Inc. for charging wait-time fees to passengers with physical disabilities.

The suit, filed in the U.S. District Court for the Northern District of California, alleges that the company violated the Americans with Disabilities Act for charging fees to passengers who, because of disability, need more time to enter a car.

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The Justice Department said Wednesday that it was suing Uber Technologies Inc. for charging wait-time fees to passengers with physical disabilities.

The suit, filed in the U.S. District Court for the Northern District of California, alleges that the company violated the Americans with Disabilities Act for charging fees to passengers who, because of disability, need more time to enter a car.

An Uber spokesman called the government’s lawsuit surprising and disappointing, and said the company had been in talks with the Justice Department about how to address its concerns. “We recognize that many riders with disabilities depend on Uber for their transportation needs, which is why we had been in active discussions with the DOJ about how to address any concerns or confusion” about the fees, the spokesman said.

The Justice Department said that Uber began charging passengers wait-time fees in a number of cities starting in April 2016 and then rolled them out more widely. The fee kicks in two minutes after a standard Uber arrives at a pickup location and is charged until the car begins its trip. Uber said the average wait-time fee charged to riders is less than 60 cents.

“Uber’s wait time fees take a significant toll on people with disabilities,” Acting U.S. Attorney Stephanie M. Hinds for the Northern District of California said in a statement.

The Justice Department is asking the court to order Uber to modify its wait-fee policy, and pay unspecified monetary damages and civil penalties, among other measures.

The Uber spokesman said the company changed its policy last week to waive the fee for any rider who said they were physically disabled.

Shares in the company were down more than 5% in Wednesday trading.

The case is the latest legal battle for Uber. In August, a California judge said that a 2020 ballot measure that allowed Uber, Lyft Inc., DoorDash Inc.

and others to continue treating their drivers as independent contractors in the state was unconstitutional. Uber and others joined forces on the ballot measure after California sought to reclassify their drivers as employees. The companies are appealing the ruling.

Uber lost a driver reclassification battle in the U.K. earlier this year, forcing the company to offer new benefits to drivers there such as paid vacation days and pension contributions.

Its food-delivery arm is in the crosshairs of regulators too. In September, Uber Eats, DoorDash and Grubhub Inc. sued New York City over a law that seeks to permanently cap the commissions food-delivery apps can charge restaurants.

Write to Preetika Rana at preetika.rana@wsj.com