The 48-hour shut down called by Kuki Students Organisation brought life to a grinding halt in Churachandpur district on Thursday.
All marketplaces in the town were deserted and attendance in government and private offices was nil. Schools and colleges also remained shut, officials said.
KSO Churachandpur branch secretary Minlal said the shutdown from midnight of Wednesday was called in protest against the deployment of additional police commandos in Moreh town in Tengnoupal district, where a sub-divisional police officer was shot dead on October 31, and for the injustices meted out towards Kuki-Zo tribal communities.
He claimed police ransacked, looted and burnt down houses and vehicles belonging to Kuki-Zo people at Sinam village along the Indo-Myanmar road in Tengnoupal district.
He also condemned the way police conducted all-out search and combing operations in Kuki-Zo inhabited Moreh town.
In a statement on Wednesday, KSO had said it took "strong exception to the continued stationing and additional deployment of Manipur police commandos in Moreh town despite Union Home Minister Amit Shah's assurance to withdraw all state forces within three days during his visit to the border town".
Shah visited the town bordering Myanmar in late May, weeks after the ethnic strife began in the northeastern state.
The Indigenous Tribal Leaders Forum, another organisation of the Kuki-Zo community, also levelled similar allegations.
The state has remained gripped by recurring bouts of violence since ethnic clashes first erupted in May. More than 180 people have been killed since then.
Meiteis account for about 53 per cent of Manipur's population and live mostly in the Imphal Valley, while tribals, which include Nagas and Kukis, constitute 40 per cent and reside mainly in the hill districts.