Putin and Castro, 87, talked for nearly an hour about international affairs and the global economy, Xinhua reported citing a Russian media report.
The reunion between the two leaders had been announced in advance by the Kremlin, though the official itinerary of the trip submitted to Cuban media did not mention it.
Castro retired from power in June 2006, after a life- threatening intestinal affliction, but he continues to be consulted on the economic and social affairs of the country. He regularly meets visiting personalities and heads of state.
On Friday, Putin paid tribute to the Internationalist Soviet soldiers who died in the line of duty in Cuba during the 1960s and 1970s.
Russia has decided to forgive 90 percent of Cuba's debt to Moscow, the Kremlin press service said on Friday, the same day of Putin's arrival in the Cuban capital Havana.
The Russian and Cuban governments signed a protocol in October regarding the debt, which amounted to 35.2 billion dollars dated from the second half of the 20th century, when the Soviet Union was a key ally of Cuba.
The remaining 10 percent of the debt will be restructured and paid over the next 10 years, and the money will be reinvested into the Cuban economy.
The announcement came on the same day when Russian President Vladimir Putin arrived in Cuba early Friday for an official visit to the island, the first stop of his Latin America tour, Xinhua reported.
Putin will travel next to Argentina on Saturday and Brazil on Sunday, to attend the 2014 World Cup final.
He will remain in Brazil to take part in the 6th BRICS Summit of emerging economies (Brazil, India, China, Russia and South Africa) in the northeastern city of Fortaleza July 15 and 16.
Russia earlier written off debts worth 116 billion dollars to countries such as Afghanistan, Mongolia, North Korea, Syria, and Libya.