In an email to The Canadian Press, spokesman Kevin Dove says nearly 60,000 polo shirts were ordered for volunteers.
The garments were produced in China by Canadian affordable apparel brand Joe Fresh.
Dove says the "minor wear" was first noted on April 28 after a paid staffer at the Uniform Distribution and Accreditation Centre washed the uniform.
He says this prompted further testing and the decision to update the logo on all of the polo shirts.
Dove says the new shirts will be delivered as soon as possible.
More than 23,000 volunteers are expected to take part in the Games.
Toronto and the surrounding area will play host to the Pan Am Games from July 10 to 26.
The Parapan American Games run from Aug. 7 to 15.
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