Immediately afterwards he went into domestic isolation, a Health Ministry report said.
“So far he has only developed cold symptoms. All contact persons will be kept informed,” it read. However, it did not provide any information on how Spahn might have been infected.
Photos show that Spahn attended a cabinet meeting on Wednesday morning at the Chancellor's Office, but he was wearing a face mask.
A government spokesperson later said that cabinet members would not have to go into quarantine, as social distancing and hygiene measures continued to be maintained.
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Spahn has been lauded for his calm handling of the virus crisis, and was once seen as a contender to take over as chancellor when Merkel stands down next year.
Spahn has welcomed stronger restrictions imposed by some states in Germany as the country tries to curb a second wave of Covid-19.
The Alpine district of Berchtesgaden in southern Germany, a beauty spot popular with tourists, on Tuesday became the first area to return to strict lockdown since the height of the pandemic earlier this year.
Last week, Germany reported its highest number of new virus cases in a single day as numbers surged across Europe.
On Wednesday Germany exceeded the coronavirus critical value of more than 50 infections per 100,000 residents in seven days on Wednesday.
The current value on Wednesday afternoon stood at 51.3, up from 48.6 on Tuesday, according to the Robert Koch Institute (RKI).
Recently, top politicians had to quarantine themselves because of encounters with those who tested positive for the virus.
On Saturday German president Frank-Walter Steinmeier also went into self-isolation following a positive coronavirus test from his bodyguard. Two tests at the head of state have since been negative.
On Monday Labour Minister Hubertus Heil of the Social Democrats (SDP) also went into quarantine because of a warning he received on Germany’s Corona-Warn-App.
At the end of September, Foreign Minister Heiko Maas (SPD) and Economics Minister Peter Altmaier (CDU) also temporarily isolated themselves, after one of Maas’ bodyguard’s was infected.
As a precautionary measure, Altmaier went into quarantine after an EU minister who was present with him at an EU Council meeting in Berlin tested positive.
Back in March, German Chancellor Angela Merkel went into quarantine after her doctor tested positive for the coronavirus. However, the Chancellor confirmed she was not infected following two negative test results.