University Hospital Galway has lost its accreditation for BowelScreen, the national programme for testing to detect bowel cancer.
UHG and Mercy University Hospital Cork have both lost their external accreditation mark due to long waiting lists.
There were 14 hospitals around Ireland contracted to carry out colonoscopies by BowelScreen.
But according to the Irish Independent the HSE has confirmed that UHG and Mercy Hospital no longer have the external quality mark for performance and standards.
However a spokesperson said that both hospitals provide an excellent service based on their detection rate and the number of completed colonoscopies.
Their units will continue to remain active and testing for bowel cancer despite this change in the accreditation status.
The spokesperson said this was similar to the UK approach, not to suspend services because of a breach in waiting times,
BowelScreen sends a home test kit to people aged 60-69 and requests that they send a stool sample back.
They then send that sample into the hospital for bowel cancer testing.
The BowelScreen programme in under increasing pressure due to Ireland’s aging population and a lack of capacity.
According to reports, BowelScreen has brought in a private contractor to tackle long waiting times.
The HSE has said that during certain periods in this year and last all hospitals that perform colonoscopies were forced to stop testing.
However the Health Executive said that this was a normal part of operations and to be expected.
Seasonal factors, annual leave, or an unexpected jump in the number of referrals could impact on the length of lists or result in cancellations the HSE said.