The routine influenza (H1N1) surveillance in India started almost a decade ago. The fluctuation in the number of deaths and cases in different Indian states over the last decade presumably indicated the possible changes in the viral sequence and in the immune response of the host. To track these changes, we have chosen NS1 protein that invades host antiviral immune response. Objective of this study was to identify the recent mutations on NS1 protein from Indian isolates. The sequences of NS1 proteins from H1N1 strains isolated in India over a decade were obtained from publicly available databases. Multiple sequence alignment, phylogeny and surface hydrophilicity analyses were performed to confirm the consistent mutations on NS1 protein, evolved chronologically in India. Total eight mutations were identified, two in RNA-binding domain (RBD), five in effector domain (ED) and one in the linker region. Three mutations were reported first time in this study at the sequence positions, 2, 80 and 155; those evolved either in 2017 or in 2019. These recent mutations were associated with conservative substitutions in the alternative domains of NS1 protein, namely, i) D2E and E55D, ii) T80A and A155T and iii) E55K and K131E. A gradual shift of NS1 antigenic regions (surface hydrophilicity) was observed from ED to RBD domains along the time line. The possible consequences of these mutations on host-pathogen interactions were hypothesized based on the sequence positions of NS1 mutations belonging to various cellular-binding sub-domains. The hypothesis is subject to further experimental and computational verification.