In given article the problem of incompleteness of the accounting data in complicated systems in sphere of public health is considered. Principal causes of this problem are analyzed on an example of the system of monitoring of the PNP «Health» (Priority national project, «Health»). The solution for elimination of incompleteness of the accounting data is suggested with the help of application of methods of the Data Mining. Results of application of the offered method to the accounting data of system of monitoring of the PNP «Health» are received. The analysis of accuracy of the offered solution is carried out.