The effect of disorder caused by MeV heavy ion irradiation on the tunnel magnetoresistance (TMR) of magnetic tunnel junctions is investigated. Two types of tunnel junctions, viz. Co/Al$_2$O$_3$/Ni$_{80}$Fe$_{20}$ and Co/Gd-doped Al$_2$O$_3$/Ni$_{80}$Fe$_{20}$ are studied. Upon 70 MeV Si ion irradiation at a fluence of $5\times10^{11}$ ions/cm$^2$, the undoped junctions show relatively small but irreversible change, while the Gd-doped junctions show a huge reduction, in TMR. In both cases junctions were completely destroyed by 200 MeV Ag ion irradiation at a fluence of $1 \times 10^{11}$ ions/cm$^2$. The results are attributed to the modification of the barrier and the neighboring interfaces caused by the high energy density deposited by incident ions.