The use of administrative documents to communicate and leave record of business information requires of methods able to automatically extract and understand the content from such documents in a robust and efficient way. In addition, the semi-structured nature of these reports is specially suited for the use of graph-based representations which are flexible enough to adapt to the deformations from the different document templates. Moreover, Graph Neural Networks provide the proper methodology to learn relations among the data elements in these documents. In this work we study the use of Graph Neural Network architectures to tackle the problem of entity recognition and relation extraction in semi-structured documents. Our approach achieves state of the art results on the three tasks involved in the process. Moreover, the experimentation with two datasets of different nature demonstrates the good generalization ability of our approach.