A study was carried out to optimize the deacidification process for noni (Morinda citrifolia L.) extract using packed column of calcium carbonate. The experiments were based on a 3-level factorial design to study the optimum process of deacidification for M. citrifolia extract. The M. citrifolia extract was treated with CaCO3 packed in different column diameter (20, 25 and 30 mm), height of calcium carbonate (0, 0.5 and 1 cm) and feed rate (10, 30 and 50 ml/min). Physico-chemical characteristics which include pH, titratable acidity, turbidity, total polyphenol content and total soluble solids were measured. Results showed that only pH, titratable acidity and turbidity could be well represented using statistical models. For pH, only the effect of height of CaCO3 was found to be significant. While for titratable acidity and turbidity, effects of diameter column and height of CaCO3 were significant. The optimum conditions for the deacidification of M. citrifolia extract was by using a column diameter of 30 mm, CaCO3 height of 1 cm, and a feed rate of 50 ml/min.