The unusual case came to light last week when Argentine police said they had seized nearly 400 kilograms (880 pounds) of cocaine worth some $62 million (€50 million) hidden in suitcases in the Russian embassy school.
Russia's ambassador had raised the alarm after discovering the drugs in December, prompting the joint operation by the two countries' law enforcement agencies.
Three Russians, including the embassy's former maintenance manager, were detained in Moscow in December, the ministry said. Argentina has also detained two suspects.
A sixth man, Kovalchuk, was believed to be the man who ran the smuggling ring.
On Thursday night, Berlin forces swooped on the alleged mastermind.
“He is now in police custody,” said a Berlin police spokesman.
Prosecutors in Berlin said the 49-year-old Russian national was detained as part of an international investigation spearheaded by Moscow.
“The allegation: founding of a criminal organisation with the aim of smuggling cocaine from Argentina to Russia,” said the prosecutors on Twitter.
Russian news agency Interfax, quoting a source close to the Russian investigation, said Moscow would seek the extradition of Kovalchuk, and that proceedings “could take months, maybe more”.
The case has sparked controversy in Russia, where the media has raised questions over contradictory official accounts of the joint operation snaring the drug ring.
Argentina's Security Minister Patricia Bullrich had claimed the gang had sought to use the Russian diplomatic courier service to fly the cocaine to Europe. But Russia's Foreign Ministry denied that the diplomatic pouch was involved in the plot.
After Argentinian police tweeted images of a Russian aircraft used in the sting operation that bears the number of security council chief Nikolai Patrushev's plane, the Kremlin denied involvement of any of its fleet.
Questions were also raised over the whereabouts of the cocaine, with some reports speculating that it had been flown to Moscow in the sting operation, even though Argentinian police said the drugs had been replaced by flour.
Russian Deputy Foreign Minister Sergei Ryabkov on Wednesday lashed out at what he called “targeted efforts to smear” the operation, RIA Novosti state news agency reported.
Ryabkov attacked journalists and bloggers for what he described as “dreaming up all kinds of non-existent versions”.
Argentinian investigators believe the cocaine, described as of “very high purity”, likely originated in Colombia or Peru.
It was destined for Russia as well as likely Germany, where Kovalchek lives.