 On 25 May 2016, he took oath as the Minister for Industries and Sports under the new Kerala Cabinet led by Pinarayi Vijayan.On 14 October 2016, he resigned over nepotism following allegations that he appointed his own family members as heads of public sector undertakings in the state.In September 2017, the Vigilance and Anti-Corruption Bureau (VACB) acquitted Jayarajan in the nepotism case and sought to close the case.