Micro-Pattern Gaseous Detectors (MPGDs) such as Micromegas or GEM are used in particle physics experiments for their capabilities in particle tracking at high rates. Their excellent position resolutions are well known but their energy characteristics have been less studied. The energy resolution is mainly affected by the ionisation processes and detector gain fluctuations. This paper presents a method to separetely measure those two contributions to the energy resolution of a Micromegas detector. The method relies on the injection of a controlled number of electrons. The Micromegas has a 1.6-mm drift zone and a 160-$\mu$m amplification gap. It is operated in Ne 95~\%-iC$\mathrm{_4}$H$\mathrm{_{10}}$ 5~\% at atmospheric pressure. The electrons are generated by non-linear photoelectric emission issued from the photons of a pulsed 337-nm wavelength laser coupled to a focusing system. The single electron response has been measured at different gains (3.7 10$\mathrm{^4}$, 5.0 10$\mathrm{^4}$ and 7.0 10$\mathrm{^4}$) and is fitted with a good agreement by a Polya distribution. From those fits, a relative gain variance of 0.31$\pm$0.02 is deduced. The setup has also been characterised at several voltages by fitting the energy resolution measured as a function of the number of primary electrons, ranging from 5 up to 210. A maximum value of the Fano factor (0.37) has been estimated for a 5.9~keV X-rays interacting in the Ne 95~\%-iC$\mathrm{_4}$H$\mathrm{_{10}}$ 5~\% gas mixture.