The case is one of the first in Europe involving a new mutation of the bacterium, which has triggered a significant surge in infection in Australia.
Known as ribotype 244, this emerging strain of C.diff is from the same family as the bug which sparked a deadly outbreak at the Vale of Leven Hospital in West Dunbartonshire in 2007.
DNA sequencing has shown similarities with that aggressive form, ribotype 027.
Government agency Health Protection Scotland (HPS) said the patient became unwell after being transferred from one hospital in Scotland to another in a different health board area. He or she is now recovering and is due to be discharged shortly. The patient and the hospitals have not been identified.
Two cases of the new strain have been reported in England, but as yet there has not been significant spread of the infection in the UK. It began emerging last year in Australia and has spread across several states.
Dr Camilla Wiuff, healthcare scientist at HPS, said: "The strain has the ability to spread in the patient population. That is why we are giving a heads-up – so the health service and hospitals know that it has come to the UK."
C.diff is a bacterium found in the gut which rarely causes problems, but it can make people unwell when it grows unchecked.
Taking antibiotics can disturb the normal balance of gut bacteria and allow C.diff to thrive, making people ill with diarrhoea and in some cases severe inflammation of the bowel, which can be life-threatening.
Some types of C.diff are particularly good at surviving, such as the 027 strain, which Dr Wiuff said was now much better controlled in Scotland.
Dr Wiuff said: "There are no implications [from ribotype 244] for the population of hospital patients as yet, but we will keep an eye on it and monitor it very closely.
"We have the same infection prevention measures for all ribotypes – trying to manage the patients in a sensible way. If they are still having diarrhoea, we put them in isolation rooms and monitor their antibiotic use."
Strict hand-washing regimes are also crucial for staff looking after sufferers. Dr Wiuff said soap and water, rather then alcohol hand gels, were required.
Rates of C.diff infections in Scotland have fallen considerably since a peak in 2007, with significant decreases reported last year, particularly among the over-65s. The total number of new cases identified in this age group in 2011 was 1465, a 34% drop on 2010.
Leading microbiologist Professor Hugh Pennington said it would be impossible to eradicate the bug.
Asked about the arrival of the new strain, Mr Pennington said: "I think one just shrugs one's shoulders and says we have not seen the back of C.diff and the main message is we never will.
"It occurs in nature. It will always be an issue, but it will be less of an issue if we have very good hospital hygiene."
The Vale of Leven outbreak, which involved 55 patients and 18 deaths, is the subject of a prolonged public inquiry.
Michelle Stewart – a spokeswoman for the C.diff Justice Group who lost her mother-in-law, Sarah McGinty, in the outbreak – said: "I would hope that the NHS is on the ball and is already working so that we do not get to outbreak levels [with the new strain].
"But let's get the inquiry reported as soon as possible so we can learn the deeper lessons."