“In the name of the PKK I want to apologise to the German people. Such things will never happen again,” said Bayek in an interview with television broadcaster Westdeutscher Rundfunk (WDR).
The organisation was banned in Germany in 1993 after it organised numerous attacks on Turkish officials, civilians and property on German territory.
In one high profile incident, Kurdish separatists occupied the Turkish consulate in Munich, taking 50 officials hostage.
The PKK has been involved in peace negotiations with the Turkish government since 2013, when imprisoned leader Abdullah Öcalan called on his militia to put down their arms.
Rolf Mützenich, deputy leader of the Social Democratic Party (SPD), said that Bayek's comments marked a significant change in attitude from the organisation.
“These comments set a new tone and offer the chance for a re-evaluation of the situation, so long as the PKK credibly and verifiably give up violence,” he said.
The change, he said, was partly due to the PKK's role in fighting Isis, with whom they are currently involved in bitter gun battles in the Sinjar region of north Iraq.
The conflict between the PKK and the Turkish state lasted over 30 years and led to the loss of over 40,000 lives.
Commenting on the PKK's stance towards Turkey, Bayik said “We don't want to fight with Turkey anymore. We say: Nothing comes from fighting. We haven't achieved our targets and nor has the Turkish state.”