The near-collision occurred early on Friday afternoon in international airspace when a Swedish SAS plane took off from the Copenhagen Airport.
Russia's defence ministry did not deny that its plane was in the area of southern Sweden at the time, but said that it was at a safe distance of more than 70 kilometres from the flight path of the passenger jet.
Swedish pilots have suggested that it was much closer.
A spokesperson from the Foreign Department was tight-lipped about the meeting shortly after the ambassador left, but said proceedings were "straightforward".
"He has been here and was met by the cabinet secretary Annika Söder," Charlotta Ozaki Macías said.
She said the department "takes the incident seriously and wants to avoid anything similar going forward".
Earlier in the day, Sweden's Foreign Minister Margot Wallström told reporters in Brussels that Swedish authorities would make their protests clear.
Danish authorities also called in the Russian ambassador, reported The Local Denmark, with both countries promising to tackle the incident together.
Foreign Minister Margot Wallström. Photo: TT
Denmark's Foreign Minister Martin Lidegaard added that the Russian pilots were "unreasonable to put civilian lives in danger".
The Russian plane was "invisible" at the time of the near-miss, as it was flying without a transponder – an electronic identification device that would have made it visible on the radar of the commercial plane.
Sweden's Defence Minister Peter Hultqvist said that such actions were "downright dangerous".
The incident marked the second this year of its kind. In March, another SAS plane with 134 passengers was "just seconds" from crashing into a Russian plane, a pilot told the Dagens Nyheter newspaper.
There has been growing concern in the Baltic region over signs of more assertive Russian behaviour, including Russian planes regularly skirting or violating the national air space of neighbouring countries.
Russia's annexation of Crimea and its involvmement in the conflict in eastern Ukraine has led to speculation that the Kremlin may be testing the
mettle of Baltic Sea countries with an uptick in airforce activity.