Packed with vitamin C, fresh orange juice is widely regarded as a healthy drink to enjoy at breakfast or on a summer's day.
They called for caterers to ensure machines are thoroughly cleaned and to serve the drink immediately after squeezing.
Under EU food regulations, 43 per cent contained ‘unacceptable’ levels of enterobacteriaceae, the bacteria family which includes Salmonella and E.coli.
The scientists also found that one in ten samples contained unacceptable levels of mesophilic bacteria, which thrives at room temperature.
The problem is believed to be down to caterers squeezing a large amount of juice at one time and leaving it in stainless steel jugs where it heats up, allowing bacteria to thrive.
Salmonella was found in 0.5 per cent of the samples, and Staphylococcus aureus - which can cause unpleasant skin infections - was found in one per cent of them.
More than 80 per cent of juice kept in metal jugs contained unacceptable levels of enterobacteriaceae, compared to just a fifth of juice samples served in a glass.
Study author Isabel Sospedra, whose findings were published in journal Food Control, said: 'Some orange juice is consumed immediately after squeezing but many cases it is kept unprotected in stainless steel jugs.
'We found that some juices that were kept in metal jugs presented unacceptable levels of enterobacteriaceae in 81 per cent of cases and in 13 per cent of cases with regards to mesophilic aerobic bacteria.
'However, when the freshly squeezed juice is served in a glass, these percentages fall to 22 per cent and two per cent respectively.'
She added: 'Juicers and juicing machines have a large surface area and lots of holes and cavities. This promotes microbial contamination, which is picked up by the juice as it is being prepared.
'To ensure consumer health, we recommend that juicers are cleaned and disinfected properly. The same goes for the jugs in which the juice is stored, although its consumption is better as and when it is squeezed.'
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