More from the NYT:
A king makes a powerful change, for stability
French officials twist US arms in bank inquiry
Fearing converts to terrorism, France intercepts citizens bound for Syria
Early last Friday, authorities in Canada, France, Germany, Luxembourg, Ukraine and the United Kingdom physically took over the servers that served as the backbone for GameOver Zeus and CryptoLocker, Ms. Caldwell said. All Internet traffic was then rerouted, under a court order, to the government's safe computer.
All weekend, the agents waited and watched for signs of success. Investigators worked from command centers at F.B.I. headquarters in Washington, Europol headquarters at The Hague in the Netherlands and at the National Cyber-Forensics & Training Alliance in Pittsburgh.
One by one, computers across the world contacted the government's safe computer, signifying that America, not the hackers, was in control of the network. With each electronic ping, the government collected the Internet addresses of the infected systems, providing a map of the worldwide infection.
By Sunday, officials said they were confident they had dismantled the network and collected enough data to help security firms and technology companies clean infected computers.
Read More'Cyber Monday': Over 131 million Americans to shop online
"More than 300,000 victim computers were freed from the botnet," Ms. Caldwell said. "We expect that number to increase as additional computers are powered on and connect to the Internet this week."
CryptoLocker similarly came under United States control, Ms. Caldwell said.
On Monday, the government unsealed court documents charging Mr. Bogachev with bank, computer and wire fraud. The F.B.I. placed Mr. Bogachev on its list of most-wanted cybercriminals.
Mr. Bogachev remains free and the United States has asked Russian authorities to turn him over. Those discussions are continuing, the Justice Department said.