We established and evaluated a flask air sampling system on a cargo C-130H aircraft, as well as a trace gas measurement system for the flask samples, as part of a new operational monitoring program of the Japan Meteorological Agency (JMA). Air samples were collected during each flight, between Kanagawa Prefecture (near Tokyo) and Minamitorishima (an island located nearly 2000 km southeast of Tokyo), from the air-conditioning system on the aircraft. Prior to the operational employment of the sampling system, a quality assurance test of the sampled air was made by specially coordinated flights at a low altitude of 1000 ft over Minamitorishima and comparing the flask values with those obtained at the surface. Based on our storage tests, the flask samples remained nearly stable until analyses. The trace gas measurement system has, in addition to the nondispersive infrared (NDIR) and vacuum ultraviolet resonance fluorescence (VURF) analyzers, two laser-based analyzers using wavelength-scanned cavity ring-down spectroscopy (WS-CRDS) and off-axis integrated cavity output spectroscopy (ICOS). Laboratory tests of the laser-based analyzers for measuring flask samples indicated relatively high reproducibility with overall precisions of less than ±0.06 ppm for CO2, ±0.68 ppb for CH4, ±0.36 ppb for CO, and ±0.03 ppb for N2O. Flask air sample measurements, conducted concurrently on different analyzers were compared. These comparisons showed a negligible bias in the averaged measurements between the laser-based measurement techniques and the other methods currently in use. We also estimated that there are no significant isotope effects for CH4, CO and N2O using standard gases with industrial isotopic compositions to calibrate the laser-based analyzers, but CO2 was found to possess isotope effects larger than its analytical precision