The company said there was no threat to health in what is being viewed as a small-scale problem.
It said it expected to start supplying the speciality spirit brand again on Monday, two weeks earlier than initial reports suggested.
Commercial director Simon Moppes said: “We have discovered a fluctuation in the coconut flavour in some production lots of Malibu.
“The affected products have been extensively tested and we have found no indication of any harm to health, but the product does not taste as it should.
“We have identified the problem to certain batches that have been distributed mainly in Europe.”
The company said it did not expect to recall stock already in the trade.