Forecasting aftershock probabilities, as early as possible after a main shock, is required to mitigate seismic risks in the disaster area. In general, aftershock activity can be complex, including secondary aftershocks or even triggering larger earthquakes. However, this early forecasting implementation has been difficult because numerous aftershocks are unobserved immediately after the main shock due to dense overlapping of seismic waves. Here we propose a method for estimating parameters of the epidemic type aftershock sequence (ETAS) model from incompletely observed aftershocks shortly after the main shock by modeling an empirical feature of data deficiency. Such an ETAS model can effectively forecast the following aftershock occurrences. For example, the ETAS model estimated from the first 24 h data after the main shock can well forecast secondary aftershocks after strong aftershocks. This method can be useful in early and unbiased assessment of the aftershock hazard.