"There is no uncertainty about the preparations," Benedict's spokesman Federico Lombardi said at a press conference.
"The Holy See is doing everything to make sure the trip takes place as planned" on September 14-16.
But he cautioned that "the future is not in our hands".
The Vatican Insider website said the Holy See's "reticence at giving precise details of the voyage is telling of a desire to move slowly in a regional situation that is becoming more explosive daily".
I.MEDIA, an agency specialising in Vatican news, had said Wednesday that the unrest in Syria and its impact on Lebanon had put Benedict XVI's visit in doubt.
It "could be cancelled at the last minute", according to unnamed sources quoted by the agency.
There are fears at the Vatican that the conflict -- which activists say has claimed more than 14,400 lives since the Damascus regime began cracking down on protests in March last year -- could spill over into northern Lebanon.
Top UN officials have described the situation there as a full-scale civil war.
Alberto Gasbarri, who is in charge of the logistics of the pope's travels, will head to Beirut by the end of June to plan the visit.
The trip will mark the second to the region for Benedict, who was in Jordan, Israel and the Palestinian territories in 2009.
Some 35 percent of Lebanon's population are Christians.