Variational Autoencoders (VAEs) have become increasingly popular in recent years due to their ability to generate new objects such as images and texts from a given dataset. This ability has led to a wide range of applications. While standard tasks often require sampling from high-density regions in the latent space, there are also tasks that require sampling from low-density regions, such as Morphing and Latent Space Bayesian Optimization (LS-BO). These tasks are becoming increasingly important in fields such as de novo molecular design, where the ability to generate diverse and high-quality chemical compounds is essential. In this study, we investigate the issue of low-quality objects generated from low-density regions in VAEs. To address this problem, we propose a new VAE model, the Latent Reconstruction-Aware VAE (LRA-VAE). The LRA-VAE model takes into account what we refer to as the Latent Reconstruction Error (LRE) of the latent variables. We evaluate our proposal using Morphing and LS-BO experiments, and show that LRA-VAE can improve the quality of generated objects over the other approaches, making it a promising solution for various generation tasks that involve sampling from low-density regions.