Mukherjee was in Hamburg on Tuesday.
He met his Chinese counterpart Yang Jiechi on the sidelines of the Asia Europe Meeting.
During Mukherjee's first meeting with the new Chinese foreign minister, the two sides also decided to convene an early meeting on the recently-established Defence Dialogue Mechanism and continue high-level contacts.
The meeting comes on the heels of China denying visa to an IAS officer from Arunachal Pradesh on the grounds that Beijing considers the state its own territory.
Beijing's decision prompted the government to cancel the mid-level training programme under which 107 IAS officers were to go to China.
During the meeting, Mukherjee and Yang reviewed bilateral ties in the light of the 10-pronged strategy to strengthen that was spelt out during President Hu Jintao's visit to India in November 2006.
Mukherjee is likely to meet Pakistan Foreign Minister Khurshid Kasuri to finalise the finer details of Prime Minister Manmohan Singh's visit to Pakistan.
Image: EU Foreign Policy Chief Javier Solana, Mukherjee and Pakistan Foreign Minister Khurshid Kasuri share a laugh before the first working session of the 8th ASEM Foreign Ministers Meeting.
Photographs: John Macdougall/AFP/Getty Images
Also see: Hu Jintao in India