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The ministry officially notified Apple earlier in the day and the company was given 10 days to respond, according to the G1 news website.
Product prices in Brazil must be quoted using the real, since charging in a foreign currency is illegal in the country.
The ministry also asked Apple to provide information on whether its service complies with the local consumer protection regulations for online stores which was updated in May.
If Apple fails to respond within the allotted time, it may have to pay a fine of up to six million reals ($2.6 million), according to G1.
Customers have been required to pay in dollars only with international credit cards after the iTunes store became available in Brazil in 2011.
The company’s online App Store for iPhone and iPad users also charges local consumers in dollars, said the website.
Brazil’s real has been falling against the dollar faster than many emerging market currencies.
The central bank is offering the equivalent of $2 billion of foreign-exchange swaps each week and $1 billion of dollar loans under a plan scheduled to run through the end of the year.