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The market is believed to have been set up by Ross Ulbricht, using Tor to hide it from online searches and the virtual currency Bitcoin to enable transactions.
Commenting on the arrests, Andy Archibald, head of the NCA’s National Cyber Crime Unit (NCCU), said the investigation will provide further insights into how criminals use the hidden internet.
He said Tor represents a challenge to law enforcement around the world, but the NCA has proved with Silk Road that it can infiltrate that environment, according to the Telegraph.
However, he said the NCA recognises the benefits of communicating anonymously online, and those engaging in legitimate business using Tor need not worry.
While services such as Tor are used for legitimate purposes such as communications between journalists and whistleblowers, they are also used for fraud and trafficking in people, drugs and other illicit goods.
More on cyber crime
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- UK government announces Cyber Crime Reduction Partnership
- Infosec 2013: Cyber crime challenges law enforcement
- Banks to test cyber defences
- Tougher EU penalties for cyber crime not enough, say security experts
Archibald said the NCA is not interested in those who use Tor for legitimate purposes, but said the Silk Road arrests prove criminals cannot use Tor to operate anonymously.
He said the NCA plans to build relationships with "trusted global partners" to share intelligence and resources to fight cyber crime.
The NCCU brings together specialists from the Police Central e-Crime Unit (PCeU) in the Metropolitan Police Service and the cyber division of the Serious Organised Crime Agency (Soca).
Archibald has indicated that the NCCU plans to take a more proactive approach to fighting crime, using all the technical and legal resources it can to disrupt criminal business processes.
In addition on focusing on the deep web, the NCA is to lead a multi-agency team, working with international partners, to fight the threat to the UK from virtual currencies, according to The Guardian.
US authorities seized Bitcoins worth $3.6m from the operation, estimated to have enabled around $1m in drug sales a month.
Virtual currencies such as Bitcoin, e-gold and Liberty reserve have been key to the establishment of anonymous online marketplaces such as Silk Road.