Quantifying spectroscopic flux variations between JWST NIRISS and NIRSpec: Slit losses in emission line measurements of z ∼ 1-3 galaxies

We analyse James Webb Space Telescope (JWST) Near Infrared Imager and Slitless Spectrograph (NIRISS) and Near Infrared Spectrograph (NIRSpec) spectroscopic observations in the Abell 2744 galaxy cluster field. From approximately 120 candidates, we identify 12 objects with at least two prominent emission lines among [O II] λ3727, H β λ4861, [O III] λ4959, [O III] λ5007, and H α λ6563 that are spectroscopically confirmed by both instruments. Our key findings reveal systematic differences between the two spectrographs based on source morphology and shutter aperture placement. Compact objects show comparable or higher integrated flux in NIRSpec relative to NIRISS (within 1σ uncertainties), while extended sources consistently display higher flux in NIRISS measurements. This pattern reflects NIRSpec’s optimal coverage for compact objects while potentially undersampling extended sources. Quantitative analysis demonstrates that NIRSpec recovers at least 63 per cent of NIRISS-measured flux when the slit covers >15 per cent of the source or when Re < 1 kpc. For lower coverage or larger effective radii, the recovered flux varies from 24 per cent to 63 per cent. When studying the H α λ6563/[O III] λ5007 emission line ratio, we observe that measurements from these different spectrographs can vary by up to ∼0.3 dex, with significant implications for metallicity and star formation rate characterizations for individual galaxies. These results highlight the importance of considering instrumental effects when combining multi-instrument spectroscopic data and demonstrate that source morphology critically influences flux recovery between slit-based and slitless spectroscopic modes in JWST observations.