This week’s budget saw funding for MRSA screening and initiatives to improve hospital cleanliness, such as paying for extra staff, slashed from £28.4 million to £18.5 million in 2014/15.
The Scottish Government said they were now able to deliver the same results for lower costs, following higher investment to kickstart the initiatives.
But Scottish Labour criticised the cut, while the Scotland Patients Association said they would be concerned if it led to a reduction in staffing levels.
The funding is used as part of the screening of patients for MRSA when they are admitted to hospital, as well as paying for infection control staff and other healthcare-associated infections initiatives.
In recent years cases of MRSA and C difficile have decreased significantly, however infections such as the winter vomiting bug have continued to plague hospitals.
Scottish Labour’s Health spokesman Neil Findlay said funding for the initiatives needed to go up if bugs like MRSA were to be eradicated from hospitals.
“Nicola Sturgeon pledged to protect hospital cleaning but Alex Neil thinks now’s the time to cut the budget by a third, that’s baffling to me,” he said.
“This sends out completely the wrong message to the public as it appears the government is saying the problem has been fixed so they don’t have to put any more money in to it, but the evidence suggests that is far from the case.
“Our hospitals have to be ready to deal with any potential bug outbreaks over the winter and they need the government’s support to do that.”
Dr Jean Turner, of the Scotland Patients Association, said: “Everyone should by now know how to do their jobs properly so we can reduce the risk of infections.
“But I would be concerned if there was any cuts to the MRSA screening or to staff numbers.”
Health Secretary Alex Neil said they were now delievering “the required outcomes and outputs for less cost”.
“Investment to tackle Healthcare Acquired Infections is driven by the rolling HAI Delivery Plan and can vary from year to year,” he said.
“The programmes, including MRSA screening, required substantial start-up investment, and planned expenditure reflects that these activities are now firmly embedded in activity of health boards.”