The HSE has warned it will slash funding at St James and St Vincent's from next week if both hospitals don't comply with rules on public pay.
According to the Irish Independent, both hospitals have been told funds will be cut by 20% if senior managers pay isn't brought in line with pay caps.
The controversy over salary top ups broke in December last year - after it emerged that executives at both the CRC and St Vincent's got top ups from private sources.
It's feared cuts will badly impact patient care.