The comment came in a statement released after Khodorkovsky left prison in St Petersburg yesterday and went straight to the city's airport, where a jet was waiting for him. Germany's Foreign Ministry confirmed later that he had landed at Schoenefeld airport.
A spokesman for energy consultants and charter flight operator OBO Bettermann, said Hans-Dietrich Genscher - Germany's foreign minister in the 1980s and 1990s - had asked for a plane after Mr Putin announced Khodorkovsky would be pardoned.
Russia's Federal Penitentiary Service said in a statement that Khodorkovsky had petitioned to be allowed to travel to Germany to meet his mother who is reportedly being treated for cancer.
He said: "I am very much waiting for the minute when I can embrace my nearest and personally shake the hands of all my friends and colleagues."
In his 10 years in prison on politically tinged charges of tax evasion and embezzlement, 50-year-old Khodorkovsky turned from a powerful oligarch into a respected dissident, becoming a political thinker who argued for social justice and placed the blame on Mr Putin for Russia's stagnating economy. It wasn't clear whether Khodorkovsky would continue his opposition to the Kremlin.
Mr Putin's announcement on Thursday that Khodorkovsky would be pardoned appeared to catch both the public and Khodorkovsky's lawyers by surprise. His release was equally shrouded in mystery. Several hours before, Khodorkovsky's lawyers and family said they still had no idea when he would be let out.
Khodorkovsky's father, Boris, speaking by phone from the Moscow region said he and his wife, were in Moscow and were going to fly to Germany today.
Khodorkovsky's second wife and three children live in the Moscow region. His eldest son from the first marriage lives with his family in New York City.
Mr Putin told reporters on Thursday that Khodorkovsky applied for the pardon because his mother's health is deteriorating. The Kremlin's website later published a decree saying that Mr Putin was "guided by the principles of humanity" when he decided to pardon Khodorkovsky.
The pardon appeared to be a sudden turnaround for the Kremlin, which has vigorously prosecuted Khodorkovsky since his arrest in 2003, in what has widely been considered to be Mr Putin's retribution for the tycoon's political ambitions.
The development - with an amnesty for two jailed members of the Pussy Riot punk band and the 30-member crew of a Greenpeace protest ship - appears aimed at easing international criticism of Russia's human rights record ahead of February's Winter Olympics in Sochi, Mr Putin's pet project.
Khodorkovsky was Russia's richest man, worth billions of dollars, and the CEO of the country's largest oil company when he was arrested at a Siberian airport and charged with tax evasion.
During Mr Putin's first term as president, the oil tycoon angered the Kremlin by funding opposition parties and was believed to harbour personal political ambitions. His actions defied an unwritten pact between Mr Putin and a narrow circle of billionaire tycoons, dubbed "oligarchs," under which the government refrained from reviewing privatisation deals that made the group enormously rich.
Khodorkovsky's company Yukos was effectively crushed under the weight of a £17 billion back-tax bill. Yukos was sold off, mostly to state oil company Rosneft, allowing the Kremlin to reassert control of the country's oil business and stifle an inconvenient voice.