The International Civil Aviation Organization has established new regulatory standards for emissions certification of non-volatile particulate matter (nvPM) from aircraft turbine engines. The adoption of the nvPM emissions regulatory standards required development of a standardized sampling and measurement methodology, and rigorous testing. Three reference systems for aircraft engine nvPM emissions measurement, compliant with the specifications for the standardized methodology, were independently developed. This paper reports the results of the first inter-comparison of these three reference systems using a CFM56-7B26/3 aircraft engine to establish repeatability and intermediate precision of the sampling and measurement systems as part of the multi-agency international collaborative projects: Aviation-Particle Regulatory Instrumentation Demonstration Experiment (A-PRIDE) 5/Studying, sAmpling and Measuring of aircraft ParticuLate Emissions (SAMPLE) III - SC03. The instruments used in the three reference systems recorded nvPM mass and number concentration, which were converted to their respective emission indices for comparison. The reference systems generally agreed to within 15% of the average nvPM number emission index and 30% of the average nvPM mass emission index. The only exception was for the nvPM mass instruments, which exhibited a higher variation as the concentration levels approached the limit of detection. The additional measured particle size distributions could be approximated to lognormal distributions with the geometric mean diameter ranging from 15 nm to 38 nm, and the geometric standard deviation varying between 1.53 and 1.92. The results from this study are a benchmark for the variability in standardized sampling and measurement systems for measuring aircraft engine nvPM emissions.