The intelligence allowed investigators to understand the illicit activity of people using the system and showed the scale of criminal businesses operating across multiple countries.
French and Dutch police said they hacked the EncroChat network so they could read millions of messages "over the shoulders" of criminal suspects as they communicated, leading to more than 100 arrests.
EncroChat delivered a message to its 60,000 users in the month of June notifying them to get rid of their devices as its servers had been "seized illegally by government entities".
However, British police have made 746 arrests, claimed 54 million pounds (A$97.4 million) in criminal cash, seized 77 firearms, including an assault rifle and sub-machine guns, and more than two tonnes of drugs, the NCA said. Those agencies will continue to use all the means at their disposal to target organised crime groups.
An estimated 60,000 people, among them up to 10,000 in Britain, subscribe to Encrochat, which works on customised Android phones and, according to its website, provides "worry-free secure communications". NCA deputy director Matt Horne said: "This is very much about the organised crime gangs operating on street corners, on estates and across communities across the entire United Kingdom".
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The Europe-wide operation took three months to complete has had the biggest known impact on gangs of organized criminals.
She went on: "By monitoring thousands of handsets and analysing millions of messages we have already mitigated threats to life including conspiracy to murder we have protected the public by taking unsafe firearms and drugs off the streets and we have seized millions of pounds in criminal cash and assets".
The force's police commissioner Cressida Dick said in a statement: "This operation is the most significant activity, certainly in my career, we have ever carried out against serious and organized criminality across London".
"By working together we have penetrated organised criminal networks who thought they were untouchable by seizing significant amounts of criminal cash, stopping firearms and drugs reaching our streets to protect the people of Northern Ireland".
Det Ch Supt Andrew Freeburn said that detectives from the PSNI's Criminal Investigations Branch had been working with the NCA and Her Majesty's Revenue and Customs (HMRC) over the last few months.
"The national dismantling of EncroChat is also a huge boost for those of us in law enforcement and our efforts to be one step ahead of organised criminals".
She added: "If you have one of these devices be very anxious because we are probably coming for you".