The Seoul Central District Prosecutors' Office said it has formally assigned the case to the intellectual property-related crime unit, Yonhap news agency reported late on Saturday.
The launch of the probe comes a day after Seoul-based civic group, Citizens United for Consumer Sovereignty (CUCS), filed a complaint with prosecutors against Apple CEO Tim Cook and Daniel Dicicco, head of Apple Korea.
CUCS has said the deliberate deterioration of older iPhones through software updates was a scam aimed at boosting sales of new models.
It claimed that the US smartphone maker should be charged with fraud, property damage and obstruction of business by digital devices.
The consumer advocate group also filed a compensation suit against Apple and its local headquarters last week, seeking an award of 2.2 million won ($2,057) per plaintiff.
Apple admitted on December 20 that its operating software updates slowed down the iPhone 6, 6S and iPhone SE, to prevent the smartphones from shutting down abruptly.
On December 28, the company denied that the measure, not disclosed to iPhone users, was motivated to induce users to switch to newer models.