Alex Neil officially opened the Royal Victoria Building in Edinburgh on Tuesday - and breached NHS guidelines by sitting on a patient's bed.
The new building was designed with single rooms throughout, rather than shared wards, to reduce the risk of healthcare associated infections (HAIs).
A Scottish Government spokewoman said: "Photographers asked Mr Neil to sit on a bed during a visit to the new Royal Victoria Building. Mr Neil was aware of safety and cleanliness protocols for visitors, as he said at the time - but it was fine for the photograph to go ahead because the bedding was due to be changed in any case immediately after his visit."
The incident was exposed at First Minister's Questions today during an exchange about Scotland's battle against HAIs.
Cases of deadly superbug MRSA have reduced by 81.5% in the last seven years, from 1,002 cases in 2005 to 185 last year, but Alex Salmond said more can still be done.
Conservative deputy leader Jackson Carlaw, the party's health spokesman, said: "Can I wholeheartedly applaud the success of the Government and the focus it has brought to this issue, both the current Cabinet Secretary and his predecessor and congratulate all of those in the NHS who have made the progress they have.
"The First Minister, I wonder, would he respond to the following that I received this morning: 'As a nurse, I was rather disgusted to see the Scottish health minister park his backside on a patient's bed while opening a new hospital and wittering on about infection control.'
"Can I implore the First Minister to implore his colleagues to desist?"
Mr Salmond said: "It's absolutely true that one of the successes has been to instil changed behaviour on the part of patients, visitors, and staff through the NHS, and that includes Government ministers.
"In future, every single one of us should aspire to the high standards of Jackson Carlaw."
The NHS offers guidance to people visiting someone in hospital.
Under the heading "What not to do when visiting someone in hospital", the first piece of guidance states: "It's best not to sit on the patient's bed as this can spread germs. Use the chairs provided."