Security forces which tried to quell the mob were forced to use force and fired tear gas shells at the mob at New Checkon in Imphal, they added.
This is the first known instance of drones being used to drop bombs on civilians by insurgents in India.
Two bodies, including that of a woman, with bullet wounds were recovered in Imphal East and West districts in Manipur, police said on Thursday.
Hours before the clashes, a planned mass burial of Kuki-Zomi people killed in Manipur's ethnic violence was stalled after the state's High Court on Thursday morning ordered status quo to be maintained at the proposed burial site in Churachandpur district.
Seven people, including a six-year-old boy, were seriously injured in a bomb blast carried out by suspected militants in Manipur's Imphal West district on Saturday.
Three persons including a 23-year-old-woman were injured after suspected militants launched a fresh bomb attack using a drone in Manipur's Imphal West district, police said on Tuesday.
Officials added that one INSAS light machine gun was recovered by the forces during initial search.
Gunmen, who are yet to be identified, arrived in camouflage dresses in the Lilong Chingjao area, and opened fire targeting locals, they said.
The withdrawal of Assam Rifles comes at a time when several groups of women in valley districts launched a demonstration on Monday, demanding the removal of the paramilitary force from the ethnic strife-torn northeastern state.
Three persons were killed and four others injured in a gunfight between two armed groups in Manipur's Imphal West district on Monday morning, police said.
The police killed a former People's Liberation Army militant and arrested 10 others, belonging to different insurgent organisations, since Tuesday.
The militants fired indiscriminately from hilltop positions towards the low-lying valley areas of Koutruk and neighbouring Kadangband killing the woman and injuring four others, including her eight-year-old daughter and a police officer.
A fresh cycle of violence erupted in Manipur last Monday after 11 suspected militants, who allegedly attacked a police station and adjoining CRPF camp with sophisticated weapons in Manipur's Jiribam district, were killed in an exchange of fire.
The Imphal Valley in Manipur remained peaceful but tense on Friday, however intermittent gunfights between militant groups and security forces were reported from the hill districts surrounding the valley.
The militants armed with sophisticated weapons surrounded the villagers of the Khamelok area bordering Imphal East district and Kangpoki district and launched the attack at around 1 am, the police said.
Curfew was imposed on Saturday night in two districts in Manipur as violence escalated on the first day of an indefinite bandh called to protest alleged molestation of a film actress by a Nationalist Socialist Council of Nagaland-Isak Muivah militant.
The use of drones to mount attacks was new to the ethnic clashes in Manipur that left over 200 people dead since May last year.
So far, over 30 people have died across Northeastern states due to heavy rainfalls, floods and landslides, according to media reports.
The incident took place as several dozens of armed men opened indiscriminate fire on Koutruk village in the periphery of Imphal Valley from the adjoining hills in Kangpokpi district, a police officer said.
The injured were later safely evacuated to Imphal for treatment. Condition of the one of them is serious, officials said.
Violent protests over the death of two youths in Manipur continued till the early hours of Thursday with a mob vandalising the deputy commissioner's office in Imphal West and torching two four-wheelers, officials said.
A class XI student was killed after school students demanding implementation of Inner Line Permit system in Manipur clashed with police.
Security forces columns, which were immediately deployed in these "vacant" villages, responded cautiously to avoid any collateral damage.
Prime Minister Narendra Modi is scheduled to visit Mizoram, Manipur, Assam, West Bengal, and Bihar to launch infrastructure projects, participate in Bhupen Hazarika's birth centenary, and attend the Combined Commanders' Conference.
The latest clashes began after the army and para-military forces commenced combing operations to de-arm communities in order to bring peace, officials said.
Operations are underway to trace three women and three children, who have been reported missing since the violence erupted in Jiribam on Monday, IGP (operations) IK Muivah said.
Drones are a new technology added recently to the weapons used in the violence between the two large ethnic groups -- Meitei and Kuki -- in the northeastern state, which left over 200 people dead since May last year.
The Armed Forces (Special Powers) Act, 1958, was completely withdrawn in Meghalaya in 2018, Tripura in 2015 and Mizoram in the 1980s.
A journalist was killed in police firing on the second day of the indefinite strike in Manipur called by a film body demanding the arrest of a Naga militant for allegedly molesting a film actress.
The villagers were venting their anger after militants burnt down at least 100 abandoned houses including the residence of Sugnu Congress MLA K Ranjit at Serou in Kakching district on Saturday midnight.
Two abandoned houses were set on fire by unidentified people in Manipur's Imphal West district in the early hours of Wednesday, an official said.
There was a brief lull between 3 am and 6 am, but the sounds of indiscriminate firing from Phayeng and Singda villages in the Kangchuk area along the two districts resumed after that.
The Manipur police said all personnel of the force from top to bottom are united and any attack on anyone and use of social media to target any officer or unit will be taken seriously and stringent action will be taken.
Meira Paibis, a collective of Meitei women, on Friday staged sit-in demonstrations across five districts of Imphal Valley in protest against the alleged gang rape of a 37-year-old woman in Churachandpur on May 3, when the ongoing ethnic violence started.
In separate incidents, automatic gunfire was reported from Kwakta in Bishnupur district of Manipur and Kangvai in Churachandpur district through the night.
A shutdown has been observed since 5 am on Tuesday in Kuki-Zo majority areas in the hills to protest against the killing of suspected insurgents, the officials said.
Attempts to resume Manipur State Transport (MST) services on Saturday suffered a setback after buses heading from capital Imphal to the hill districts could not go beyond Imphal valley.
Eight firearms and 112 rounds of ammunition were recovered from different districts of violence-hit Manipur during search operations by security forces, police said.
Two Central Reserve Police Force personnel also sustained injuries during the heavy exchange of fire that happened at Jakurador Karong in the Borobekra sub-division, they said.
At Thamnapokpi under Moirang constituency in Bishnupur district, armed men fired several rounds in the air near a polling booth prompting voters to flee, police said on Friday, adding additional security personnel were rushed to the spot to contain the situation.
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