The theory of fuzzy soft as well as intuitionistic soft set generally depends on complete information. But there are situations in which the complete information is not available due to various different reasons like data erroneous, in sufficiency of data, lacking of evidence and illegibility of data. Missing data restrict fuzzy soft matrix and intuitionistic fuzzy soft matrix and that causes more ambiguous uncertainty in the process of decision making. Thus, estimation of incomplete information data plays an important role in multi criteria decision making process which has been developed recently.  Here, a novel method of missing data estimation in intuitionistic fuzzy soft matrix is described. Firstl, we estimate the missing values using the information given in data. After estimation the missing values in IFSM thus obtained is applied in a multi-criteria decision-making problem with illustration by an example.