Good lens hygiene is important in preventing infections which could lead to keratitis and damage eyesight permanently.
Lens users are supposed to disinfect them nightly in a solution which often includes the powerful chemical hydrogen peroxide.
However, scientists from the Department of Medical Parasitology in Vienna University, Austria, found that conventional solutions were having little effect on a particular bug called acanthamoeba.
This single-celled organism is resistant to eradication because it can take two forms, an active "tropozoite" and a far less active "cyst".
Resistant to disinfectant
The cysts are far more sluggish, reproducing less frequently and prove far less susceptible to the poisons contained in the lens solutions.
The Austrian researchers found that while, after eight hours soaking, all the solutions had killed all the trophozoite forms of the bug, some cysts were able to survive an eight hour soaking with some of the solutions.
Most effective, they said, was a "two-step" solution containing 0.6% hydrogen peroxide.
A multipurpose non-peroxide solution did not perform as well, killing cysts from some strains of the bug.
However, a one-step peroxide solution performed poorly, with cysts from all strains still alive after an eight-hour soak.
This means that in theory, they could live on and continue to reproduce in the film of neutralised solution left in the contact lens cases from day to day.
Wearers of soft lenses are thought to be at the greatest risk of serious eye infection - which is a frequent cause of damaged eyesight.
Microwave method
The authors of the research, writing in the British Journal of Ophthalmology, suggest that users choose their lens solution carefully, and keep their lens cases as free of colonisation as possible by frequently microwaving, boiling or changing them.
Mr John Dart, an expert in eye disease at the Institute of Ophthalmology and Moorfields Eye Hospital in London, said that the organism was able to live on in the "slime" left inside contact lens cases.
He told BBC News Online: "At the moment there are no standards which include acanthamoeba for contact lens solutions.
"The organisms which live in this slime metabolise far more slowly, and there is a lot of data showing how resistant they have become to disinfectants.
"None of the solutions work very well in the contact lens case."