Apple is appealing the ruling and said in a statement, "we respectfully disagree with the determination" of the Russian anti-monopoly service.
Russia has imposed a $12.1 million fine on Apple for "abusing" its dominant position in the market by giving preference to its own applications, a government regulator said.
The move comes as Russia ratchets up pressure against Western tech companies, with authorities aiming to bring the Russian segment of the internet under state control.
It also comes as antitrust agencies in the European Union, the United States, Britain and South Korea take increasing interest in Apple, with firms wanting to break free of the terms of its global app store.
"Apple was found to have abused its dominant position in the iOS distribution market through a series of sequential actions which resulted in a competitive advantage for its own products," Russia's Federal Anti-monopoly Service said in a statement.
It said that it had hit the company with a fine of more than 906 million rubles after ruling in favour of a complaint brought against the US tech giant by cybersecurity company Kaspersky Lab.
Apple is appealing the ruling and on Tuesday said that "we respectfully disagree with the determination" of the Russian anti-monopoly service.
The company added that it is "proud to have helped hundreds of thousands of developers in Russia, including Kaspersky reach more than one billion customers in 175 countries through the App store."
READ MORE: France slaps Apple with record $1.22B fine
'The anti-Apple law'
A new law went into effect in Russia earlier this month demanding that smartphones, tablets and computers sold in the country come with pre-installed domestic software and apps.
Dubbed the "anti-Apple" law, the controversial bill was introduced in an effort to promote Russia's tech companies but critics say it is the latest attempt to tighten state control over the internet.
It requires all devices with internet access sold in the country, whether they are produced locally or abroad, to be equipped with approved software produced by Russian companies or face fines starting in July.
The list includes programmes made by Kaspersky.
Apple reportedly voiced strong opposition to the legislation and threatened to pull out of the Russian market, but eventually agreed to comply.
Russia routinely fines Western tech companies like Apple, Google and Facebook for failing to comply with its legislation.
It has blocked a number of websites that have refused to cooperate with the authorities, such as LinkedIn.
In March it began throttling Twitter's service speeds, accusing it of failing to remove content related to child pornography, drug use and calls for minors to commit suicide.
In recent years, the Russian government has also been tightening control over the internet under the pretext of fighting extremism and protecting minors.
In 2019, it passed a law on the development of "sovereign internet" aimed at isolating the country's internet from the worldwide web, a move activists say will stifle free speech.