Glasgow Life said inaccurate electronic counting systems could be why it failed to hit visitor targets for 2009-10.
The nine museums run by the service attracted three million visitors during the last financial year, nearly 140,000 fewer than forecast.
Scotland’s most-visited attraction, Kelvingrove, suffered the biggest drop. This trend continued during the summer, with visitor numbers 28% below target in July.
A spokesman for Glasgow Life said subsequent manual counts suggested figures might be “substantially” off.