The breakfast juices stop the drugs from entering the bloodstream and getting to work in the body - potentially rendering them useless.
The researchers said the potential effects were so serious, that if in doubt, people should swap their fruit juices for water when on medication.
Researcher David Bailey said: 'This is just the tip of the iceberg. I'm sure we'll find more and more drugs that are affected this way.'
Twenty years ago, the same researcher showed that grapefruit juice dangerously magnifies the effect of the blood pressure drug felodipine - a finding that led to warnings that the drink should be avoided by those on some medicines.
The latest study shows fruit juices can also cut the power of medicines - potentially stopping them from doing any good.
Professor Bailey, of the University of Western Ontario in Canada, said: 'The concern is loss of benefit of medications essential for the treatment of serious medications.'
Drugs so far shown to be weakened by grapefruit, orange and apple juices include the blood pressure-lowering beta blockers atenolol, celiprolol, and talinolol and the hay fever treatment fexofenadine.
The popular antibiotic ciprofloxacin is also affected, as are the cancer drug etoposide and a drug given to prevent transplanted organs being rejected.
But many other drugs are also likely to be affected, an American Chemical Society conference has heard.
The researcher, a professor of pharmacology, advised patients to speak to their doctor or pharmacist before taking fruit juice with their medicines.
Most medications should be taken with water, he said.
Professor Bailey made the link after asking a group of volunteers to take the hay fever drug fexofenadine at the same time as either a glass of water or a glass of grapefruit juice.
Taking the drug with the juice cut its absorption into the bloodstream by half.
Experiments showed that naringin, the chemical behind the grapefruit's bitter taste, blocked the drug from moving from the small intestine into the bloodstream.
The researchers have pinpointed a naringin-like compound in orange juice and are looking for a similar one in apples.
A different mechanism is at play with the drugs whose levels are boosted by grapefruit juice. There, the juice inactivates a liver enzyme that breaks down drugs, turning normal doses into potential overdoses.
The study is far from the first to link supposedly healthy juices with dangers.
Last month, research from the respected Harvard Medical School in the US, showed that just one glass of orange juice a day can significantly increase the risk of the form of diabetes linked to poor diet and obesity.
Eating whole pieces of fruit however, cuts the likelihood of developing the disease.
Also research at the University of North Carolina two years ago showed that a substance in grapefruit juice could cause dangerous side effects when ingested with certain drugs.
Certain medications administered to patients for control of blood pressure and cholesterol and other drugs if consumed along with grape fruit juice could cause unhealthy and even dangerous side effects, it was said.
The drugs affected by grapefruit juice usually have some difficulty entering the body after they are consumed because an intestinal enzyme, CYP3A, partially destroys them, as they are absorbed. Grapefruit juice, but not other commonly consumed fruit juices, inhibits this enzyme, allowing more of these drugs to enter the body.