During the phase when stars appear in the Hertzsprung-Russell-Diagram in the upper asymptotic giant branch (AGB), they loose, due to a wind driven by pulsations, at least half of their mass. The inner part of the envelop thus formed, also called extended atmosphere, is expected to bear complex magneto-hydrodynamic phenomena, due to the interaction of the wind with the previously expulsed matter and, possibly, with Jovian or terrestial planets. As in the solar system, fluctuations of the magnetic field (''space weather''about a mean value can be expected, but the observational evidence is still lacking. Here we show that for a narrow range of velocities the circular polarization of SiO masers, tracing the magnetic field in the extended atmosphere of AGB stars, varies in two stars with a period of a few hours. Previous multi-epoch observations of SiO masers were neither polarimetric nor critically sampled to detect such intraday magnetic fluctuations. Because statistically significant fluctuations are seemingly rare and localized in the extended atmosphere, they are expected to be due to a variety of phenomena. Coronal flux loops, magnetic clouds or Jovian magnetospheres provide suitable explanations. Our study opens the way to future observations combining intensive full polarization monitoring of SiO masers, sampling at least once per hour, with high spatial resolution. This will ultimately allow us to distinguish between the proposed scenarios and to investigate the fate of inner planetary systems around solar-type stars entering their AGB phase.