Hybrid integration of photonic chips with electronic and micromechanical circuits is projected to bring about miniature, but still highly accurate and reliable, laser spectroscopic sensors for both climate research and industrial applications. However, the sensitivity of chip-scale devices has been limited by immature and lossy photonic waveguides, weak light-analyte interaction, and etalon effects from chip facets and defects. Addressing these challenges, we present a nanophotonic waveguide for methane detection at 3270.4 nm delivering a limit of detection of 0.3 ppm, over 2 orders of magnitude lower than the state-of-the-art of on-chip spectroscopy. We achieved this result with a Si slot waveguide designed to maximize the light-analyte interaction, while special double-tip fork couplers at waveguide facets suppress spurious etalon fringes. We also study and discuss the effect of adsorbed humidity on the performance of mid-infrared waveguides around 3 μm, which has been repeatedly overlooked in previous reports.