Since 20016, Istat has been carrying out the Permanent Census of Non-Profit Institutions on an annual basis. This is a register-based census that relies on the Non-Profit Institution Statistical Register (NPISR). The NPISR is created by integrating several administrative archives and survey data and by applying statistical tools to identify active institutions. Every three years, Istat carries out a sample survey to collect information on thematic issues and to evaluate the over-coverage of the statistical register. In 2022, Istat conducted a supplementary survey to estimate the under-coverage. The paper illustrates the results of the two surveys on the over- and under-coverage of the NPISR. Furthermore, it presents a strategy to use these results to improve the statistical tools for identifying active institutions and to reduce the over- and under-coverage of the NPISR.