The quality of the software has an increasing impact on the performance, operation and ultimately the cost of industrial automation systems. Software metrics are necessary to assess the quality and to identify modules that impact cost of testing and maintenance. There is a number of software metrics available within a software engineering domain. However, there is a gap when it comes to evaluating IEC 61499 automation software. It is a challenging task too. IEC 61499 architecture embraces several software development techniques such as imperative languages, state machines and object oriented programming. This paper proposes the method for calculating metrics for IEC 61499 function blocks. These metrics were used to analyze power system protection software. Metrics confirmed expected results and reasonably described quality of software modules. With further improvement and expansion of the proposed set of metrics, it will be possible to accurately analyze and therefore improve automation software design and reduce cost.