The Jack and Jill Foundation is urging the Health Minister to give all seriously ill children medical cards.
The charity says it is extremely disappointed that only youngsters with cancer are being given the cover.
It was revealed earlier this week that children under 18 who have been diagnosed with cancer will be issued with medical cards for five years.
The change came into effect automatically from July 1st.
However CEO of Jack and Jill - Jonathan Irwin - is asking Minister Leo Varadkar and the HSE why medical cards are not being issued automatically to all children qualifying for the domiciliary care allowance.
He says that while it is 'absolutely right' that children with cancer are protected, it is unfair to single out one group of vulnerable children:
Mr Irwin added, "this just doesn’t make sense medically, morally or financially and what rubs salt into the wound is that it comes against the backdrop of healthy children under six being given a free GP card automatically, while the families of children who most need medical support, outside of cancer, still being subjected to torturous means testing."
The HSE has said the number of discretionary medical cards issued has increased from 52,000 to 87,000 to date - with further increases expected.
The organisation says children with disabilities have been particularly targeted, to ensure that no child is denied access to necessary healthcare.