Objectives. To describe the monitoring model of the Health Care Service Institutions (HCSI) of the National Health Authority (NHA) and assess the factors associated with risk-adjusted normative compliance (%RANC) within the Peruvian Health System (PHS). Materials and Methods. We carried out a case study of the experience of the NHA in the development and implementation of a monitoring program based on the ISO 31000-2009. With HCSI as the units of analysis, we calculated the %RANC (a score in continuous scale ranging from 0 to 100) for comprehensive monitoring (CM) and for specific evaluations made from 2013 to 2015. A higher score in the %RANC means lower operational risk. Also, slope coefficients (β) and their 95% confidence intervals (95% CI) were estimated using generalized linear models to estimate the association between %RANC as outcome, and health subsector, region, level of care and year, as explanatory variables. Results. The NHA made 1444 evaluations. For CM, only the Social Security Administration had higher %RANC than private centers (β=7.7%; 95% CI 3.5 to 11.9). The HCSI of the coastal region (β=-5.2, 95% CI -9.4 to -1.0), andean region (β=-12.5; 95% CI -16.7 to -8.3) and jungle region (β=-12.6, 95% CI% -17.7 to -7.6) had lower %RANC than those located in Lima Metropolitan area. %RANC was higher in 2015 than 2013 (β=10.8; 95% CI 6.4 to 15.3). Conclusions. The %RANC differs by health subsector, region and year of supervision. For CM, the HCSI in the Social Security Administration and in the Lima Metropolitan area had better scores, and scores improved over time. The implementation of actions aimed at improving %RANC in order to foster the full exercise of health rights in the PHS is suggested.