Imphal: The shutdown in Manipur's Churachandpur and Kangpokpi districts affected normal life on Saturday, officials said.
Markets and other commercial establishments remained shut, while vehicles stayed off the roads, they said.
No untoward incidents have so far been reported, they added.
The shutdown began in the two districts on Friday and would continue till Sunday.
The shutdown has been called by Kuki-Zo groups, including the Indigenous Tribal Leaders Forum (ITLF) and Kuki Students Organisation (KSO), in protest against Security Advisor Kuldiep Singh's statement.
Singh had on September 20 claimed that security forces have taken a number of steps in the wake of reports that "900 militants" might carry out violence in peripheral villages of Imphal valley districts.
The state government on Wednesday, however, retracted the claim and asserted that the likelihood of "any such misadventures by armed groups is minimal and unsubstantiated".