Defects are of significant importance to determine and improve the distinct properties of 2D materials, such as electronic, optical, and catalytic performance. In this report, we observe four types of point defects in atomically thin flakes of 1T-PtTe2 by using low-temperature scanning tunnelling microscopy and spectroscopy (STM/S). Through the combination of STM imaging and simulations, such defects are identified as a single tellurium vacancy from each side of the top PtTe2 layer and a single platinum vacancy from the topmost and next layer. The density functional theory (DFT) calculations reveal that the platinum vacancies from both the monolayer and bilayer exhibit a local magnetic moment. In bilayer PtTe2, the interlayer coulomb screening effect reduces the local magnetic momentum of the single platinum vacancy. Our research provides meaningful guidance for further experiments about the effects of intrinsic defects on potential functions of thin 1T-PtTe2, such as catalysis and spintronic applications.