Figures show a 6% increase in antibiotic use in hospitals and a 3% rise in prescriptions issued by GPs in the community.
Dr Camilla Wiuff, strat-egic lead for microbiology with Health Protection Scotland, said the rises were "a little bit disappointing".
An investigation into the reasons for the surge in antibiotic use in hospitals is being undertaken this year.
Dr Wiuff said there were several reasons why hospital doctors might be handing out more, including a surge in the number of elderly patients or very sick people on the wards, and larger doses being required to treat certain conditions. She also said a campaign to treat blood poisoning early could have encouraged prescribing.
The quantity of anti-biotics prescribed by GPs has fallen significantly since the mid-1990s, but began to climb again in recent years. The data, released by the information division of NHS Scotland, shows a 3.3% rise in 2012. It is the second year in a row that the figure has increased.
Dr Wiuff said that in hospitals patients some-times continued to receive antibiotics when the treatment could be stopped and regular reviews of patients' medication could ensure this did not happen.
The use of antibiotics in hospitals was up 6.2% in 2012, compared to 2011.
There is concern on an international scale about bugs evolving to resist antibiotics and the way this could weaken the ability of medicine to fight infections.