He was not behind the counter but on a computer in a separate area, according to Italian news agency ANSA.
Officers in Liguria checked in on the pharmacy as it was about to open, with customers already queueing up outside, according to a local online newspaper.
He has been charged for breaking quarantine, according to local media.
The Italian government has banned people who have been diagnosed with Covid-19 from leaving the house in a bid to tackle the spread of the disease.
Those who ignore this rule risk between three to 18 months in prison and could be fined up to €5,000 (£4,360), according to a national decree.
People who have not tested positive for the virus are allowed to go outside only if it is essential, for example to get groceries or go to work.
Police have conducted checks on more than nine and a half million people since the start of the lockdown in mid-March, according to the interior ministry.
Italy has been one of the worst-hit countries in the world during the coronavirus pandemic, with nearly 190,000 confirmed Covid-19 cases to date.
The death toll stood at 25,549 on Friday, according to official figures.
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