During bad weather conditions, muon flux above 1 GeV observed in GRAPES-3 muon telescope shows large variations. The atmospheric electric field is believed to be responsible for acceleration of cosmic ray muons. A thunderstorm event observed on 30 September 2015 is discussed here. The field of view of large area (560 m$\rm^{2}$) tracking muon telescope at GRAPES-3 allows study of muon intensity variations in 169 directions with $\sim$4$^\circ$ resolution. This event shows large decrease in North-East directions, with a maximum decrease of -0.6% in all directions combined and -4.5% in a single direction. Muons from selected directions were combined and processed with fast Fourier transform (FFT) to remove slow and ultra-fast variations ($\triangle$f = 10-200 cycles per day). The filtered data shows maximum decrease of -1.2% with statistical significance of 9$\sigma$. Monte Carlo simulations were carried out with modified CORSIKA package to incorporate electric field. Simulations show that electric potential $\sim$1 GV is needed to get variation of 1% in GRAPES-3 muon flux.