In the polluted modified bootstrap percolation model, sites in the square lattice are independently initially occupied with probability $p$ or closed with probability $q$. A site becomes occupied at a subsequent step if it is not closed and has at least one occupied nearest neighbor in each of the two coordinates. We study the final density of occupied sites when $p$ and $q$ are both small. We show that this density approaches $0$ if $q\ge Cp^2/\log p^{-1}$ and $1$ if $q\le p^2/(\log p^{-1})^{1+o(1)}$. Thus we establish a logarithmic correction in the critical scaling, which is known not to be present in the standard model, settling a conjecture of Gravner and McDonald from 1997.