Deep learning has shown promising performance in submeter-level mapping tasks; however, the annotation cost of submeter-level imagery remains a challenge, especially when applied on a large scale. In this paper, we present the first submeter-level land cover mapping of Japan with eight classes, at a relatively low annotation cost. We introduce a human-in-the-loop deep learning framework leveraging OpenEarthMap, a recently introduced benchmark dataset for global submeter-level land cover mapping, with a U-Net model that achieves national-scale mapping with a small amount of additional labeled data. By adding a small amount of labeled data of areas or regions where a U-Net model trained on OpenEarthMap clearly failed and retraining the model, an overall accuracy of 80\% was achieved, which is a nearly 16 percentage point improvement after retraining. Using aerial imagery provided by the Geospatial Information Authority of Japan, we create land cover classification maps of eight classes for the entire country of Japan. Our framework, with its low annotation cost and high-accuracy mapping results, demonstrates the potential to contribute to the automatic updating of national-scale land cover mapping using submeter-level optical remote sensing data. The mapping results will be made publicly available.