Christian Solidarity Worldwide and seven other non-governmental organisations have written to the EU abut the exclusion of many Cubans from a discussion about their human rights.
Religious leaders are often harassed in Cuba and the state makes it clear it is keeping an eye on them and their families. Some people have reported travel bans and being called in to police stations to answer questions.
A dialogue between Cuba and the EU about their human rights was agreed in 2016.
This month, Christian Solidarity Worldwide (CSW) and other charities wrote to the EU High Representative for Foreign and Security Policy, Josep Borrell, and the EU Special Representative on Human Rights, Eamon Gilmore, about misleading conduct in the EU-Cuba Human Rights Dialogue.
The NGOs say they are concerned about the exclusion of independent Cuban civil society from the process and highlight misinformation in EU communications about the bloc's most recent Human Rights Dialogue with Cuba about the extent of civil society engagement.
The EU-Cuba Human Rights Dialogue was created as a result of an agreement the EU signed with Cuba in December 2016.
One of the main components was the establishment of a "dialogue and cooperation involving stakeholders, including, as appropriate, regional and local governments, civil society and the private sector."
However, CSW argue that independent civil society has been consistently excluded from the dialogue and cooperation.
On 25th February, assurances were made that Cuban civil society would be included, but only Cuban government-approved organisations attended and no members of independent civil society on the island were allowed to participate.
In the letter, the NGOs state: "It is disappointing and worrying to see a discrepancy between the EU's standards, the political obfuscation they incur, and the EEAS reluctance to acknowledge this. Such an approach only allows violations of human rights in Cuba to continue unabated and, most unfortunately, it strengthens the repression the Cuban government exercises on individuals and organisations which are part of 'independent civil society'."
CSW's Alessandro Pecorari said: "Without robust and independent civil society engagement this aspect of EU-Cuba relations will amount to little more than a box-ticking exercise and more importantly, a betrayal of the brave individuals who risk their freedom daily defending human rights including freedom of expression and freedom of religion or belief in Cuba."