Weedy rice, particularly paddy seed, is difficult to handle and separate because it has characteristics (morphological likeness) similar to those cultivated rice. This research describes a modification of self-organizing maps (SOMs) for categorizing weedy rice from cultivated rice using near-infrared spectroscopy (NIR) on paddy seed in situ. Optical microscope and thermogravimetric analysis were employed to evaluate the physical properties and thermal behavior of rice sample, respectively. For direct sample analysis, a near-infrared spectroscopy with a reflectance attachment was used. The developed approach was performed to efficiently classify weedy rice directly from paddy seed with remarkable accuracy (91-99%). The developed approach is very effective, non-invasive, environmentally sustainable, and straightforward approaches to assess and investigate the quality of rice seed. This could potentially be applied in the future for various seed quality inspection.