The unidentified agent was in stable condition after being shot while executing a search warrant at about 7:30 a.m., said Laurie Bennett, special agent in charge of Buffalo's FBI office.
The agent was part of a group of law enforcement officers rounding up drug and money-laundering suspects.
Bennett said the shooting happened after a drug suspect was arrested at the house and investigators stayed to search the property.
Bennett did not comment on media reports that another agent fired the shot. A news conference was scheduled for Thursday afternoon.
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