Colombian President Juan Manuel Santos says he now knows why so many Colombians opposed his re-election to a second term, which he won in a hotly contested runoff in June: They didn’t trust his negotiations in Havana with the Marxist terrorist group known as the Revolutionary Armed Forces of Colombia (FARC).

Mr. Santos told me in a recent interview in New York that his government has conducted research to better understand those who did not vote for him. Many respondents, he said, had come to believe that he is “planning to give the economy to Castro and Chávez, or to get rid of the army, or to put in a FARC commander to lead the police, or to expropriate the territory around the cities.” He now realizes that he “underestimated the power of such an amount of lies” and “never thought people would believe them.”

This is why, last month, he “put the record straight by publishing what has been agreed” in the Havana talks, to show that “we are not throwing the country into the arms of communism.” Yet the release of the partial agreements may only add to Colombians’ distrust.

Secret negotiations between the FARC and the Santos government had been going on in Havana for a year before they became public in August 2012. On Sept. 4, 2012, Mr. Santos gave a speech saying “the conversations will not go on for an unlimited time. They will be measured in months, not years.” The president says now he expressed that as his “hope.” He still believes the FARC is negotiating in good faith—despite its continued attacks on civilians and infrastructure.

I asked Mr. Santos about the charge in Colombia that his negotiations put the FARC terrorists on equal moral footing with the democracy. “How very strange that the same people who say that sat down for two years with the same terrorists, or another group at the same level, the [National Liberation Army or ELN] in Cuba,” he says. “The only difference is that my predecessor failed and, so far, I have been successful.”

His predecessor, former President Álvaro Uribe, has spoken publicly in past years about his attempts to reach an agreement with the FARC to free hostages. On two occasions he extended good faith but the FARC failed to comply with its commitments. He also told me in an email that his government did indeed explore a peace dialogue with the ELN in Havana. He said that the effort was thwarted because the rebels refused his precondition that they cease their criminal activity. The Santos government did not respond to my requests for copies of the documents that Mr. Santos says show that there is “absolutely no difference” between the two peace efforts. It only sent me a rehash—in news clippings—of what is already known about Uribe initiatives.

The FARC sees a difference. In September it wrote on its website that it negotiates with the Santos government because Mr. Santos recognizes the violence as an “armed conflict” (this of course gives them belligerent status), while Mr. Uribe always insisted they were nothing but terrorists.

As to the success claimed by Mr. Santos, it still seems a long way off. Journalist María Isabel Rueda wrote in a column in the Colombian daily El Tiempo on Sept. 28 that the number of “pending” issues in the partial agreements “surprised” her. She asked Alfredo Rangel, a prominent Colombian political scientist and now an opposition senator, how important they are.

His examples of what are left to be negotiated include rural property rights, free-trade agreements, mining and energy policy, and the demilitarization of the countryside. Mr. Rangel says the agenda also still includes negotiations on the “democratization of information and communication,” which suggests greater state control of media and sounds like it is straight out of the Hugo Chávez playbook. Another goal, the “popular control of international treaties,” implies a weakening of representative government while “the total suspension of spraying” to destroy coca plants is crucial to FARC financing.

Mr. Santos also said that while there will be no impunity for those who have committed crimes against humanity, “how you define jail and what type of jail, these are the things we have to negotiate.”

Such discussions make many Colombians nervous, as does the prospect of guerrillas gaining special political rights, another topic of negotiation. Most troubling is the government’s suggestion that it could put approval of the final deal to the nation as an up-or-down vote rather than asking for approval point by point.

I asked Mr. Santos if the rebels deserved the legitimacy that the talks give them. “What would be the alternative?” he responded. “Don’t negotiate and continue living with terrorism and another 50 years of war?”

That suggests to some that the terrorists have the government just where they want it. No wonder many Colombians remain unconvinced that the country can rid itself of gangster terror through negotiations without sacrificing freedom.