The nearby (d = 19.7 Mpc) Seyfert galaxy NGC 3079 exhibits a prominent bubble emerging from the nucleus. In order to investigate the nuclear power source, we carried out ammonia observations toward the center of NGC 3079 with the Tsukuba 32-m telescope and the JVLA. The NH3 (J,K) = (1, 1) through (6, 6) lines were detected in absorption at the center of NGC 3079 with the JVLA, although the profile of NH3 (3, 3) was in emission in contrast to the other transitions. All ammonia absorption lines have two distinct velocity components: one is at the systemic velocity (V
sys ~ 1116 km s−1) and the other is blueshifted (V
sys ~ 1020 km s−1), and both components are aligned along the nuclear jets. The blueshifted NH3 (3, 3) emission can be regarded as ammonia masers associated with shocks by strong winds probably from newly formed massive stars or supernova explosions in the nuclear megamaser disk. The derived rotational temperature, T
rot = 120 ± 12 K for the systemic component and T
rot = 157 ± 19 K for the blueshifted component, and fractional abundance of NH3 relative to molecular hydrogen H2 are higher than those in other galaxies reported. The high temperature environment at the center may be mainly attributed to heating by the nuclear jets.