Eighteen Colombians, nine of whom are wanted by the US, were arrested during the worldwide investigation that began in July 2006, the attorney-general's office said.
The three Middle Eastern suspects, identified as Shekry Mahmud Harb, Ali Mohammed Abdul Rahim and Zacaria Hussein Harb, were captured on October 13 in Bogota, a source in the attorney-general's office said.
The men, who were of Lebanese and Jordanian descent, "co-ordinated the shipment of drugs to their countries of origin, and used front companies to bring the cash into Colombia", the statement said.
Some of the cash was "was distributed in Middle Eastern countries for the supposed financing of terrorist groups such as Hezbollah", it said.
Washington has often complained that Iran-backed Hezbollah and other Muslim groups that it considers terrorist organisations are active in Arab communities in South American countries such as Brazil and Venezuela.
The operation, called Titan, has already led to some 90 arrests in various countries, Colombian authorities said.
As part of the operation, police confiscated some $740,000, 360kg of cocaine and 5kg of heroin, as well as two aircraft, a boat, and various vehicles and jewels, the attorney -general's office said.
Colombia remains the world's number one cocaine producer, although over the last seven years Washington has sent more than $5bn in aid that has helped weaken the country's leftist fighters and reduce violence from its conflict.
Speaking to Al Jazeera on Thursday, Elias Hanna, a retired Lebanese army general, cast doubt on Colombia's claims that Hezbollah could be involved in the illegal drugs trade.
He said there is still no evidence, only accusations, that Hezbollah was involved.
Hanna said it was unlikely that Hezbollah, which takes pride in its image a Lebanese resistance group, would risk its reputation in such a manner.