The microchips, inserted into the neck, will allow them to keep tabs on the best animals and safeguard the gene pool of its three million-strong herd.
Alpacas, which are related to camels and produce fine wool, are increasingly popular among US and European breeders.
"We know that alpacas are being moved across the border with Bolivia and then on to Chile," Pilar Tuppia from Peru's National Council of South American Camelids told the Associated Press.
This included "unscrupulous individuals" buying top animals from poor people in the countryside, she said.
The plan is to tag some 900 top alpacas within five years.
Alpacas, along with related llamas, vicunas and guanacos, are native to South America but are increasingly popular in other parts of the world - not only for their fleeces.
They also make tasty, lean steaks.
ALPACA FACTS
Native habitat: South America
Number in S America: 3.5m
First domesticated: 4,000 BC
Adult height: 1 metre
Adult weight: 50-80 kg
Average lifespan: 15 - 20 years
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