The Rape Crisis Network of Ireland (RCNI) has said that it was no longer able to publish statistics because of funding cuts.
Since 2005, the RCNI has produced national statistics, but it will not publish a 2016 report.
In 2015, the Child and Family Agency Tusla had cut funding to the RCNI, which made up 70% of the organisation's funding, on the basis that Tusla would collect the information itself.
The RCNI said that its database continues to be promoted as best practice to other European countries.
It said it has proven that it can safely, truthfully and accurately tell survivors stories using this data, while protecting the identity of those who use the services of rape crisis centres around Ireland.
The RCNI also said that the information given by the centres to Tusla has not been "cleaned and verified" often in order to protect service users, and so Tusla cannot provide accurate statistics.
In a statement, Tusla said that it is gathering "summary data ... to allow insight into and understanding of the services delivered and the needs of survivors."
It said that "all data gathered undergoes an extensive process of cleaning and validation."
However, the statement made no mention of whether or not it would be publishing a 2016 report.
A Tusla spokesperson tonight said that the agency does intend to produce an annual report on sexual violence statistics for 2016.
The Director of the Waterford Rape Crisis Centre has said that the voice of some of the most vulnerable survivors is being lost at a national level, due to changes to the way sexual violence statistics are collected.
Anne Scully described the news that the RCNI would no longer be publishing annual national statistics as a great disappointment and a huge loss to the sector as they gave a voice to survivors.
Speaking to RTÉ News, Ms Scully said that providing information directly to Tusla instead of to the RCNI raised concerns around the privacy, confidentiality and protection for their clients.
She said: "For example if we have very small numbers or a particular population, say someone from a particular European country or somebody who is transgender, we can't pass on those numbers [to Tusla] and expect that those survivors identities will be completely safe."
She added: "There is a danger of people possibly being identified if that information is matched with other information."
"The RCNI could publish and produce that data at a national level which provided safety because there's more safety in numbers where data is concerned.
"We do not hand over small numbers to Tusla, and they know that we don't, but what that means is that the voice of those survivors, who may be among the most vulnerable survivors, is being lost at a national level."