The citadel sits atop a chasm that the former inhabitants may have used as a lookout to spy on approaching enemies, said Goicochea Perez.
Rock paintings cover some of the fortifications, and next to the dwellings are large platforms believed to have been used to grind seeds and wild plants for food and medicine, he said.
The citadel is tucked away in the remote Jamalca district of Utcubamba province, part of the northern Amazonas department, said Jamalca Mayor Ricardo Cabrera Bravo, who had joined the expedition.
The area, about 800 kilometers (497 miles) northeast of Lima, is famed for its vast, isolated natural beauty, surrounded by verdant foliage and soaring waterfalls, said Cabrera Bravo.
The citadel likely belonged to the Chachapoyas civilization -- an ancient people whose glory days over a thousand years ago pre-date the hegemony of the powerful Incas.
The Chachapoyas culture (known as the Cloud Forest people) also built the imposing Kuelap fortress atop a mountain in Utcubamba, which can only be compared in scale to the Inca's Machu Picchu retreat, built hundreds of years later.