The UK's National Crime Agency (NCA) said 14,500 people had bought spying tools from the Imminent Methods site.
Police searched more than 80 properties across the world to find those selling the tools.
They were also able to trace people who had bought the software and charge them with computer misuse offences.
Imminent Methods sold a tool known as the Imminent Monitor Remote Access Trojan (Imrat) for about $25 (£19).
It gave the attacker full access to an infected device, letting them steal data, monitor what the victim was doing and even access their webcam.
The NCA said properties in Hull, Leeds, London, Manchester, Merseyside, Milton Keynes, Nottingham, Somerset and Surrey were among those searched.
The international operation was led by the Australian Federal Police.
The authorities were able to take down the website selling the software, which subsequently stopped the cyber-stalking tools from working.
The NCA's Phil Larratt said the tools had been used "to commit serious criminality" including "fraud, theft and voyeurism".
Police said 14 people had been arrested worldwide in connection with the sale and use of the software.
By seizing control of the website, police will have been able to "take a good look at what the site has been up to, including who has bought the illegal items", said Prof Alan Woodward, a cyber-security expert from the University of Surrey.
"The authorities now know how many users bought the malware on offer. They will now be working to unmask the 14,500 who were daft enough to buy this malware."
Crime as a service
"Organised crime gangs, as well as more petty criminals, are switching their attention to cyber-crime rather than, say, drugs, because it is perceived there will be a significant return on their investment and much lower risk," said Prof Woodward.
He said in addition to selling hacking tools, criminals also provide access to the infrastructure to power their malware, including so-called bulletproof hosting.
"They set themselves up in jurisdictions and in such a technical manner that they think they are untouchable by law enforcement agencies in the countries where their clients conduct their crimes," he told the BBC.
"All of the above is called crime as a service, and has been a significant trend in recent years."