“I can honestly say that it pains me. Every day I try to build a better relationship with Russia and on the other hand there is such hard evidence that Russian forces are doing this,” she told parliament.
Germany's intelligence service has repeatedly called out attempts by Russian hackers to spy on lawmakers or leading politicians.
German media reported that among information copied by hackers in 2015 was data from Merkel's email account. That attack also targeted the Bundestag.
Merkel said investigators into the 2015 hacking had identified a specific suspect.
“Unfortunately the conclusion I have reached is that this is not new,” she said, noting that “cyber-disorientation, the distortion of facts” were all part of “Russia's strategy”.
“Obviously this doesn't make it easier” to foster a better relationship with Moscow, she said, calling such spying tactics “more than uncomfortable”.
Merkel has always stressed the importance of dialogue with Russia, even while making clear her disapproval of Moscow's actions in different arenas — from annexing Ukraine's Crimea, to cyber meddling in elections and its backing of Bashar al-Assad's government in Syria.
The rogue operation that targetted the Bundestag in 2015 involved an aggressive attack called Sofacy or APT 28 that had also struck NATO members and knocked French TV station TV5Monde off air.
According to Spiegel magazine, hackers managed to completely copy two of Merkel's email accounts containing correspondence dating between 2012 and 2015.
German media have also named the suspect as Dmitry Badin, who is also wanted by the FBI for other cyberattacks, including those targeting the Democrats during the 2016 US presidential election.
In a clear warning to Russia that their activities would not go unpunished, Merkel also pointed to last year's killing of a former Chechen commander in a Berlin park.
The shock 2019 murder has badly bruised ties between Moscow and Berlin, and German prosecutors have already said they have evidence the killing was carried out on behalf of Russian or Chechen state agents.
“It of course disrupts a cooperation of trust and you know that in connection with the murder… we applied sanctions, in this case, expulsions (of Russian diplomats),” said Merkel.
“We now have the task of finding the wanted suspect, but of course we always reserve the right to take measures — also against Russia, to be clear.”