UK groups the Open Rights Group (ORG), Statewatch and Privacy International, amongst 40 others, have submitted their arguments in support of Ireland's ongoing case to have the Directive repealed.
Ireland supports the aims of the Directive but is arguing that the way in which it was passed was wrong. It says that the process used was designed for trade and that it should have been passed through a process designed for security matters. That process is tougher, requiring a unanimous vote rather than a majority one.
The civil liberties groups want the ECJ to reject the Directive on different grounds, though.
"While it is true that there is no legal basis for the Directive, it is first and foremost illegal on human rights grounds," said the document lodged at the Court. "We urge the Court to base its decision on the incompatibility with human rights rather than the lack of competence."
The groups are worried that a rejection of the Directive on Ireland's grounds would lead to an identical law being introduced through different channels.
The Data Retention Directive requires that telecommunications companies keep records of customers' communications for up to two years. When implementing the Directive into national law, countries can choose any retention period of between six months and two years.
The records to be kept are of the fact of the communications and not their content, for example what telephone called what telephone number when and for how long, but not what was said.
The groups have argued that this retention breaches Article 8 of the European Convention on Human Rights (ECHR) which guarantees the right to respect for private life and correspondence.
"The European Court of Human Rights has repeatedly held that the metering of traffic data without the consent of the subscriber constitutes an interference with the rights to respect for private life and correspondence," said the submission to the ECJ.
"Just as the metering of telecommunications by government officials, the state-imposed retention of traffic data by private telecommunications companies is an interference with article eight of the EHCR."
The bodies also argued that the activity is in breach of Article 10 of the EHCR, which guarantees freedom of expression, including the freedom to receive and impart ideas without state interference.
"Retaining all traffic data on the population's communications would have a disturbing effect on the free expression of information and ideas," said the groups' submission.
"In comparison to the marginal benefits of traffic data retention, its negative effects on the freedom of expression are major.
Therefore, blanket data retention requirements are disproportionate and incompatible with article 10."
The groups claim that it is essential that the Directive be challenged not just on Ireland's procedural grounds, but on its more fundamental arguments.
"A decision on human rights is urgently needed to protect the privacy of telecommunications in Europe," it said.