Privacy International is challenging the bulk collection of phone records and the harvesting of data, and will take its concerns to the UK's Investigatory Powers Tribunal.
Privacy International said that its case, the first in the UK to challenge the data harvesting, follows the passing of the USA Freedom Act, and should be mirrored in the UK. The practice is enabled by a loophole, it explains, and the loop needs closing.
"Secretly ordering companies to hand over their records in bulk, to be data-mined at will, without independent sign off or oversight, is a loophole in the law the size of a double-decker bus," said Eric King, deputy director at Privacy International.
"The use of these databases - some volunteered, some stolen, some obtained by bribery or coercion - has already been abused, and will continue to be until the practice is overhauled, and proper protections put in place.
"That the practice started, and continues without a legal framework in place, smacks of an agency [GCHQ] which sees itself as above the law."
Much of the system is shrouded with darkness and a lot of it is already being challenged in the courts. King said that the US has taken the lead in this, and chided the UK for falling behind. Privacy International's legal challenge wants to see the system stopped completely.
"How can it be that the US is so much further ahead on this issue? With the USA Freedom Act now passed, the equivalent NSA power has now been curtailed before the debate this side of the pond has even begun," added King.
"Bulk collection of data about millions of people who have no ties to terrorism, nor suspected of any crime, is plainly wrong. That our government admits that most of those in the databases are 'unlikely to be of intelligence value' but that the practice has been allowed to continue shows just how off course we really are."
The UK High Court will also hear a case that challenges the Data Retention and Investigatory Powers Act (DRIPA), a piece of legislation that was adopted last year under 'emergency' conditions.
DRIPA is part of the government's push for more surveillance power and internet control. It was rushed through last July at a time when the European Commission was saying that such overzealous surveillance was inappropriate.
Rights group Liberty has now mounted a challenge to DRIPA with the support of MPs Tom Watson and David Davis.
The organisation said that the timing of the case is important because of the recent adoption of the Investigatory Powers Bill and what it describes as the gradual erosion of liberty.
"The executive dominance of parliament in rushing through this legislation using a wholly fabricated 'emergency' made a mockery of parliamentary sovereignty and the rule of law, and showed a staggering disregard for the entire population's right to privacy," said Emma Norton, legal officer for Liberty.
"It is thanks to the Human Rights Act that we are able to challenge the government's actions, the same government which now seeks to axe that very piece of legislation and, by doing so, curb the British people's ability to do so in future."
DRIPA has been roundly criticised since it was created and passed into law in just a few days last year.
To remind yourself of the controversy around DRIPA, take a look at this briefing http://t.co/d9l4CPkgoO— Big Brother Watch (@bbw1984) June 4, 2015
"Back in April, the Court of Justice of the EU ruled that the blanket retention of our data interfered with our right to privacy and should therefore be targeted where there are specific threats," said Jim Killock, executive director of the Open Rights Group last year.
"In contradiction of this judgement, the UK government has instead chosen not only to continue to retain our data but to increase the information it collects about us.
"We have a choice between blanket, pervasive and excessively intrusive surveillance that breaches everyone's right to privacy, and targeted data retention that protects our fundamental rights."
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