At issue is Apple's App Tracking Transparency policy that compels third party developers to secure an opt-in from iPhone users to track their usage for advertising and other purposes.
The policy, launched two years ago, blew a hole in Facebook's revenue and caused a tremor in the online advertising market as many users chose to disallow tracking.
According to the Italian authority, the Silicon Valley titan "has adopted a more restrictive privacy policy for third-party app developers than it applies to itself", the competition watchdog said in a statement.
It said it was also concerned third-party developers and advertisers were "disadvantaged in terms of the quality of the data made available by Apple".
The "alleged discriminatory conduct" could cause a drop in advertising revenues of third-party advertisers and prevent competitors from entering or remaining in the app development and distribution market, benefiting Apple's own apps, it added.
Apple said App Tracking Transparency rules "apply equally to all developers -- including Apple -- and we have received strong support from regulators and privacy advocates for this feature.
"We will continue to engage constructively with the (Italian authority) to address any of their questions," it said in a statement.
Apple reported profit of $24 billion on revenue of $94.8 billion in the first three months of this year.
The business practices of US big tech companies have come under growing scrutiny in Europe, leading to huge fines and legislation to curb their market dominance.
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