Correa on Wednesday denied taking money from Colombian rebels as a row erupted over the counting of votes in Saturday's referendum, with incomplete results suggesting he could lose on two key issues.

A sense of alarm in Quito deepened when a senior US counter-narcotics official said Ecuador was becoming a "United Nations" of organised crime, with drug traffickers from Albania to China using it as a staging ground for Andean cocaine.

On Tuesday the London-based International Institute for Strategic Studies published a report which claimed that the Revolutionary Armed Forces of Colombia (Farc) helped to fund the 2006 presidential campaign which brought Correa to power.

The 240-page report, based on documents seized by Colombian troops at a Farc camp in Ecuador in 2008, suggests the rebels gave more than $100,000 (£61,000). "Correa almost certainly approved the use of these funds in his campaign, but this did not translate into a policy of state support for the insurgents," said Nigel Inkster, the IISS's director of transnational threats and political risk.

Correa, 48, a left-wing US-trained economist, said he would not have accepted even 20 cents from the guerrillas. "If someone in the name of (my) campaign asked for money then the Farc was duped because we never received any money from them."

According to the report, the president hoped to broker the release of Farc hostages but communications with the rebels faded after the Colombian cross-border raid killed a senior Farc commander, Raul Reyes, and seized computers, hard drives and memory sticks.

In a separate claim, Jay Bergman, the US Drug Enforcement Administration's Andean region director, said Ecuador had become a trafficking hub for Peruvian and Colombian cocaine. "We have cases of Albanian, Ukrainian, Italian, Chinese organised crime all in Ecuador, all getting their product for distribution to their respective countries," he told Reuters news agency.

Relaxed visa regulations – part of an attempt to woo tourists – and meagre law enforcement resources helped smugglers, said Bergman. But he commended Ecuador's recent successes against traffickers. "They are doing a pretty bang up job in terms of basic interdictions with a fraction of the capabilities and the resources of the Colombians."

Correa, a popular and charismatic leader, appeared to have strengthened his self-styled "citizen's revolution" last weekend when exit polls pointed to him sweeping all 10 issues in a referendum. "We've won – thank God and the people!" he said.

By Tuesday however, with 51% of votes counted, the president appeared to be narrowly behind on two controversial issues: media regulation and a new system to appoint judges. He accused the National Electoral Council of manipulating the vote count.

Correa was suddenly on the defensive but he was a resilient and resourceful politician who thrived in counterattack, said Michael Shifter, of the Inter-American Dialogue thinktank.

"The opposition remains fragmented and Correa is still by far the most popular figure in the country. He has faced serious problems before but he has managed to overcome them by waging a permanent campaign against traditional political and economic interests. As the opposition has learned, it is a mistake to underestimate him."