The bodies of the children aged between five and 14 were found near Huanchaco, a beachside town north of capital Lima. They were believed to be sacrificed between the 13th and 15th centuries by the pre-Columbian Chimu civilization according to a state media agency.
The Chimu civilization were inhabitants of northern Peru before they were conquered by the Inca.
"This is the biggest site where the remains of sacrificed children have been found," chief archaeologist Feren Castillo told AFP news agency.
The discovery came a year after 200 bodies of children were dug up at two other sites in Peru.
Castillo said they were sacrificed to honor the Chimu ritual gods.
"It's uncontrollable, this thing with the children. Wherever you dig, there's another one," he said.
They showed signs of being killed during wet weather and buried facing the sea in an attempt to "appease the El Niño phenomenon" which means slight warming of the waters of the Pacific.
Some of the children still had skin and hair when they were dug up and archeologists are continuing excavation in anticipation of finding more children.
"Skeletal remains of both children and animals show evidence of cuts to the sternum as well as rib dislocations," read the report.
Chimu worshipped a moon god called Shi which they believed to be more powerful than the sun and regularly used child sacrifice for their rituals.
According to local news media, four mass sacrifices were made by the Chimu which involved three child sacrifices, and one using animals.
Last year April, graves of 140 children between five and 14 were found. In July same year, 56 more bodies were found.