The pandemic situation caused by coronavirus (COVID-19) which has infected more than 200 countries around the world. Every country should have strategic planning and a roadmap regarding how to stop the spread of the virus. One of those is trying to build an application to be an aggregator and a tool supporting other strategic planning. In Indonesia, Ministry of Communication and Informatics (KEMKOMINFO) has the responsibility to build the application to stop the spread of the virus and trace every movement done by the user or people. An official application built by KEMKOMINFO is PeduliLindungi. PeduliLindungi is an application that helps the government in tracking to stop the spread of Coronavirus Disease (COVID-19). On the other hand, PeduliLindungi is more complex because it involves many entities. And of course, it will cause a high impact level of Data Integration and Interoperability (DII). So, in this paper researchers will try to get all issues of DII in the PeduliLindungi application and try to analyze the system architecture and subsequently give solution to refactor the architecture used by PeduliLindungi.