Researchers studied a group of treatments known as GLP-1 agonists, used for the treatment of Type 2 diabetes.
GLP-1 agonists are a group of injectible drugs usually prescribed to patients who have not been able to bring their condition under control through lifestyle changes.
They are designed to regulate blood sugar levels both by stimulating the release of the hormone insulin which naturally controls levels.
They also work by inhibiting glucagon, a peptide which raises the concentration of glucose, or sugar, in the bloodstream.
But the study found one such treatment had the unrecognised potential to activate receptor sites for glucagon - promoting the release of sugars into the blood.
Dr Graham Ladds, from St John's College, said the results point to a lack of knowledge about the impact of the GLP1 treatments.
He said: "What we have shown is that we need a more complete understanding of how anti-diabetic drugs interact with receptors in different parts of our bodies.
"GLP-1 agonists clearly benefit many patients with Type 2 diabetes and there is no reason to presume that our findings outweigh those benefits.
"Understanding that picture, and being able to consider all the components of target cells for such treatments, is vital if we want to design drugs that have therapeutic benefits for diabetes patients, without any unwanted side effects."
The team, from Cambridge and Warwick universities, carried out a series of lab based tests on yeast and mammalian cell culture containing glucagon and found that it was activated by GLP-1 agonists.
Dr Ladds added: "The work shows that, contrary to our previous assumptions, glucagon receptors can potentially be activated by anti-diabetic treatments."
Current GLP-1 agonists available in the UK include Bydureon, Byetta and Victoza.
People with diabetes suffer from high blood sugar levels caused by their bodies not producing enough insulin, the hormone that enables the uptake of sugar from food.
Around 347 million people worldwide have diabetes and it is likely to become the seventh leading cause of death in the world by 2030.
The paper stresses these are only initial findings.