Mendis, a former Test captain, will work under the new management appointed by the government after it dismissed the elected office-bearers of the SLC in March.
"Mendis is back at work now," an official told AFP on Thursday. "His resignation was not accepted by the elected office bearers, so he is now working under the new management."
Mendis was not immediately available for comment, but he told confidants he had felt harassed by the ongoing battle for the control of the cricket body.
The island nation's cricket administration was plunged into crisis in March when sports minister Jeevan Kumaratunga suspended the elected office-bearers, citing financial mismanagement, and appointed an interim committee in its place.
Sri Lanka's Court of Appeal on Wednesday allowed the interim committee to take charge of the sport pending a final verdict on the case filed by elected SLC president Thilanga Sumathipala against his dimsisal.
The International Cricket Council last week recognised the interim committee after seeking legal advice.