"I believe that the blow we are going to give to this structure is a mortal blow. I do not believe that gangs as we know them now will exist in three or four years," Bukele said at a press conference to evaluate the progress of the first phase of a security plan launched last month.
As part of the plan, Salvadoran security forces have been targeting extortion rackets run by gangs to finance their operations.
Authorities have also declared a state of emergency in 20 prisons in the country, tightening the conditions of confinement and ordering mobile phone operators to block internet and cellphone reception in prison to keep gang members from ordering killings and extortion while behind bars.
Earlier this month, the government announced the second phase of the security plan that seeks the "territorial control" of dozens of gang-riven communities while disrupting the recruitment of young people through social programs.
El Salvador is thought to have some 70,000 gang members, of whom around 17,000 are imprisoned. Most belong to either Mara Salvatrucha (MS-13) or its rival Barrio 18.
Bukele, who took office on June 1, called for the public to collaborate with the government to stop gang violence.
"We cannot overcome this scourge alone... This is a unique opportunity we have to beat the gangs," he said, adding the security plan will include unspecified measures to be rolled out in the coming years.
El Salvador has one of the highest rates of violent crime of any country not at war, with an average of 51 homicides per 100,000 inhabitants in 2018, most of which are attributed to gangs.