The agreement, signed in April, allows US troops to deploy around the canal but not to establish bases, according to the Panamanian authorities.
The US military will train alongside Panamanian security forces in forest operations, the US embassy said in a statement to AFP Thursday.
It said the entry of American troops for military exercises had to be approved by Panama.
Panama signed the security agreement after pressure from US President Donald Trump, who threatened to take back the 82-kilometre (51-mile) waterway that connects the Pacific Ocean to the Caribbean Sea.
He has repeatedly claimed that China has too much influence over the canal, which handles about 40 percent of US container traffic and five percent of world trade.
The agreement has triggered protests from unions and other organizations, who argue that it "violates national sovereignty" and constitutes a veiled return of former military bases.
The American military has in recent years participated in several military exercises in Panama alongside other Latin American countries.
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