The hospital trust is one of a handful in the country to use the new technology in a bid to combat the spread of bugs like clostridium difficile (C diff).
But guidelines from the Department of Health, which are based on a piece of legislation from 1969, means the laundry system, called Otex, can only be used on mops and not sheets or other bed linen.
Otex artificially recreates the thunderstorm effect to generate the chemical ozone through an electric charge and is said to be 3,200 times more effective than chlorine bleach.
But the system uses cold water which goes against the 1969 rule, updated in 1995, which says all laundry and linen should be washed at 70 degrees Centigrade at least.
East Sussex Hospitals NHS Trust, which runs both the DGH and the Conquest, said it only uses Otex to clean mops.
A spokesman said, "Bed linen is cleaned by the normal hot water and detergent processes laid down by the Department of Health.
"We have our own laundry service and treat all laundry as infected and wash it at the higher temperature of 85 degrees for 15 minutes, which exceeds the standards set out."
During development of the Otex system, microbiologists examined a mop which had been used on a hospital ward and subsequently disinfected in the normal way using hot water.
They found it still had 150,000 colonies of C diff spores on it but after the mop was processed with Otex, no trace of the superbug was found.
Research has also shown the system can destroy MRSA and the winter sickness bug norovirus.
A recent study in the medical publication The Lancet showed 40 per cent of C diff infections are spread by hospital bed linen and gowns worn by patients.
Scientists have proved that standard laundry systems do not kill C diff and that it can be returned to hospital beds on apparently bug free sheets and blankets.
A Department of Health spokesman said, "The available evidence does not suggest that linen is a major source of C diff infection.
"Failure to isolate patients and inadequate cleaning of the environment are known to be major transmission routes."
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