Professor Naveed Sattar and Dr Jason Gill, from the University of Glasgow's Institute of Cardiovascular and Medical Sciences, said that drinking more than just one glass a day of fruit juice can lead to an increased risk of diabetes.
They have also argued that fruit juices should not be included in the current five-a-day guidelines as high intake is "counter-productive" to a healthy lifestyle.
Mr Sattar, who is Professor of Metabolic Medicine, said: "Fruit juice has a similar energy density and sugar content to other sugary drinks.
"For example, 250ml of apple juice typically contains 110 kcal and 26g of sugar, and 250ml of cola typically contains 105kcal and 26.5g of sugar.
"Additionally, by contrast with the evidence for solid fruit intake, for which high consumption is generally associated with reduced or neutral risk of diabetes, current evidence suggests high fruit juice intake is associated with increased risk of diabetes."
Writing in the Lancet Diabetes and Endocrinology journal, they called for more comprehensive labelling of high-sugar fruit juices to help the public make more informed decisions about their diet.
It comes amid a debate about whether sugar is as bad as tobacco or alcohol and should be treated as a public health issue in the same way.
Doctors told Westminster last month that the obesity crisis could be stopped within five years if the industry cut the amount of sugar it put into food by 30%.
Prof Sattar said yesterday: "In the broader context of public health policy, it is important that the debate about sugar-sweetened beverage reduction should include fruit juice.
"Helping individuals cut not only their excessive fat intake, but also refined sugar intake, could have major health benefits, including lessening obesity and heart attacks.
"Ultimately, there needs to be a refocus to develop foods which not only limit saturated fat intake but simultaneously limit refined sugar content."
As part of the study, the researchers also tested public awareness regarding the sugar content of fruit juices, smoothies and sugar-sweetened drinks by carrying out an online poll of more than 2000 adults.
Participants were shown pictures of full containers of different non-alcoholic beverages and were asked to estimate the number of teaspoons of sugar contained in the portion shown.
Although the sugar content of all drinks and smoothies was similar, the sugar content of fruit juices and smoothies was underestimated by 48% on average, whereas the sugar content of carbonated drinks was overestimated by 12%.
While many fruit juices are billed as containing one portion of a person's recommended daily fruit intake, it is by no means a substitute for fruit itself.
In addition to its higher sugar content, fruit juice is also without much of the natural fibre found in a piece of fruit.
However, fruit juices can contain important vitamins and minerals, whereas sugar-sweetened drinks do not.
But Dr Gill said the micronutrient content of fruit juices may not offset the "adverse metabolic consequences" of excessive consumption. He added: "There seems to be a clear misperception that fruit juices and smoothies are low-sugar alternatives to sugar-sweetened beverages.
"[But], contrary to the general perception of the public, and of many healthcare professionals, that drinking fruit juice is a positive health behaviour, their consumption might not be substantially different in health terms from drinking other sugary drinks."