Mr Naidu will first travel to Guatemala on May 6 in what would be the highest-level visit from either side.
The visit would focus on various areas of mutual cooperation such as protection of wildlife, human resource and training, and information technology among others, Preeti Saran, Secretary East in the Ministry of External Affairs, told reporters during a briefing.
During his visit, Mr Naidu will meet Guatemalan President Jimmy Morales, Vice President Jafeth Cabrera and Speaker of Parliament Alvaro Arzu Escobar.
Mr Naidu will then reach Panama on May 7 for the second leg of his visit.
In Panama, Mr Naidu will hold meetings with Panamanian President Juan Carlos Varela and Vice President and Foreign Minister Isabel Saint Malo and discuss cooperation in key areas such as agriculture, education and economic cooperation.
On the third and final leg of his visit, Mr Naidu will visit Peru.
He will hold talks with Peruvian President Martin Vizcarra and Vice President Mercedes Araoz among other leaders.
He will also attend an event to mark the 55th anniversary of the establishment of diplomatic relations between India and Peru.
The vice president's discussions with the leadership of that country will cover the entire spectrum of bilateral relations, including trade, commerce investment, IT, medicine, space, defence and culture, Ms Saran said.