The seizures were made this month in a joint operation with the U.S. Immigration and Customs Enforcement Agency, commonly called ICE.
"Forty-one million dollars is not a rounding error. The loss of that kind of money hurts," ICE Director John Morton said Monday at a news conference in Washington.
The cash, seized during five raids between Sept. 9 and Sept. 18, was found hidden aboard container ships sailing from the Port of Manzanillo, Mexico, to Buenaventura, Colombia, Morton said.
The bulk of the cash was in $50 and $100 bills, Morton told CNN in a story published Tuesday.
Smugglers use Buenaventura and Manzanillo to move cocaine north to Mexico and into the United States, with cash returning to Colombia, where most cocaine shipments originate, Morton said.
Colombia is to keep $28 million and Mexico $13 million in accordance with international laws governing where the money was seized.