Ancient pyramids at El Paraíso, above, outside Peru's capital of Lima, are at the center of a legal dispute.Ryan Dube/The Wall Street Journal
LIMA, Peru—For 4,000 years, the pyramids at an archaeological site on the edge of Lima survived earthquakes, Spanish conquistadors and a bloody revolution. But they were no match for developers cashing in on Peru's economic boom.
Prosecutors in August filed charges against a developer that Peruvian officials said used a front-loading tractor last year to level a 20-foot pyramid at El Paraíso, and planned to flatten three others to make way for housing construction.
Archaeologists say such incidents are increasingly plaguing Peru's cultural patrimony, which includes one of the world's great empires, the Incas, and several other notable civilizations. The quick rise of Peru's modern economy, they say, is colliding with the remains of ancient societies in a way that dwarfs the artifact looting that has long afflicted Peru's ruins.
"This is now a much bigger problem than looting," said Walter Alva, a Peruvian archaeologist who has made some of the most important discoveries in Peru over 30 years. "It is very difficult to juggle the protection of cultural heritage with economic interests."
Over the past decade, Peru has clocked average annual growth of more than 6%, the fastest in South America, as foreign investments in the mineral-rich nation rose from $1.6 billion in 2004 to $10 billion in 2013. The poverty rate fell to 24% from almost 60% as a bigger middle class fueled demand for homes and cars.
But the protection of Andean fortresses and pyramids has lagged behind, government officials and archaeologists say, in part blaming an archaeology budget of just $7.3 million.
Less than 20% of the 14,000 archaeological sites in the Ministry of Culture's database have been mapped—their precise boundaries marked—by authorities. Only 133 sites have been included in a land registry intended to provide them more legal protection.
The Nazca Lines, the massive drawings of animals, trapezoids and straight lines carved into Peru's southern desert 2,000 years ago, have been damaged by urban growth, unregulated mining and road construction. The Ministry of Culture plans to file at least 10 criminal charges against individuals for damaging them.
Archaeologists studying Chankillo, a fortified complex that is home to a 2,300-year-old solar observatory 250 miles north of Lima, have fought informal gold miners and roads built by asparagus farmers that destroyed part of an ancient cemetery, said archaeologist Ivan Ghezzi, who leads research at Chankillo and believes at least 30 archaeological sites are now covered by asparagus.
More than 120 miles north of Lima, the site of Cerro Colorado, part of the Caral-Supe civilization, the oldest in the Americas, was damaged in 2012 by mining and road construction. The government ordered the company to move operations from the site after pleas by archaeologists.
Advocates for preserving Peru's past say the damages to these and dozens of other sites are irreparable.
"It's like burning a book that no one will ever read," said Ruth Shady, one of Peru's best-known archaeologists and an expert on the Caral-Supe civilization. "You are losing all of the information that the book contains."
Protecting cultural heritage is a global challenge. In Belize, a Mayan pyramid was bulldozed last year by construction workers. In war-torn Syria, ancient sites have been so damaged by conflict that the United Nations describes the situation as a "cultural hemorrhage." Archaeologists in Greece say the theft of antiquities has risen after budget cuts brought on by the country's economic crisis left sites unprotected.
In Peru, the dry, coastal climate helped preserve a rich trove of fabrics, thousands of years old and made from alpaca, vicuña or cotton, as well as colorful ceramics and gold-plated jewelry. That has been a boon to archaeologists who have flocked to Peru since Hiram Bingham, an American explorer, was credited with discovering the Incan bastion of Machu Picchu in 1911.
But it is a headache for builders who face bureaucratic delays.
Contugas, a unit of Colombia's Grupo Energía de Bogotá, said it came up against 10 archaeological sites when building a 180-mile pipeline to transport natural gas to the southern city of Ica. The construction, which was completed in April, was delayed 200 days, Contugas spokesman Paul Rocca said, as the government required the company to detour around the sites.
Archaeologists say new investment projects, among them a 620-mile gas pipeline in southern Peru that will be built by Brazil's Odebrecht and Spain's Enagás, are expected to come into contact with dozens of sites.
"They are facing an incredible challenge," said Luis Jaime Castillo, an archaeologist who is deputy minister of cultural heritage in the Ministry of Culture.
During construction, companies are required to have an archaeologist on site to excavate and recover artifacts and tombs to protect them in cases where it would be unfeasible to stop or alter a project, but this causes delays.
"There is a lack of efficiency and flexibility," said Carlos Gálvez, chief financial officer of Compania de Minas Buenaventura SA BUENAVC1.VL -2.33% A, a Peruvian mining company.
The Ministry of Culture says it is working on finding a balance between protecting Peru's heritage and ensuring that archaeology isn't an obstacle to development.
Last year, in response to Contugas's delays, authorities established a 20 working day limit for the permit needed to allow a project to move forward if there were no archaeological remains on the work site. Approval used to take several months.
"Even though we have to protect as much as we can, we cannot make cultural patrimony so important that nothing can be done," Mr. Castillo said.
Peruvians have a complicated relationship with their country's archaeological heritage. Sites like Machu Picchu and the Nazca lines attract legions of foreign tourists. In Lima, diners at a high-end restaurant can enjoy traditional Peruvian seafood dishes while watching archaeologists unearth 1,000-year-old mummies of the Wari culture at a pyramid, the Huaca Pucllana.
But one woman, who the Ministry of Culture says was squatting illegally on protected land at El Paraíso, said she didn't even believe there were ancient ruins next to her home. "The ministry just wants to take over land that doesn't belong to them," she said.
Mr. Ghezzi, the archaeologist, said he and other scientists face a challenge: instilling pride among Peruvians for their history.
"Regulations mean nothing if society doesn't support the protection of our heritage," he said.
Write to Ryan Dube at ryan.dube@dowjones.com