Voting will be held in 59 seats as the polling in Williamnagar in East Garo Hills district has been countermanded following the killing of NCP candidate Jonathane N Sangma in an IED blast on February 18.
Women voters in their colourful tribal attires were seen queueing up at polling stations across the state since morning and shops in the vicinity did brisk business.
The polls will be held till 4 am across the state.
He said that six additional companies of CAPF were deployed in the troubled East and South Garo Hills districts.
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Today's polling will decide the fate of 361 candidates including 31 women and 80 Independents, election office sources said, adding 18.09 lakh voters are eligible to exercise their franchise in 3,025 polling stations in the state.
Kharkongor said the number of women candidates this time is the highest ever in the state.
State Director General of Police S B Singh said 580 polling stations have been categorised as 'vulnerable' and strict security measures are in place across Meghalaya to ensure free and fair polls.
Another 340 polling booths have been categorised as 'critical' while 67 are both vulnerable as well as critical.
The BSF has also been asked to keep a close vigil along the 443 km-long India-Bangladesh border, the CEO said.
The Election Commission has appointed in all 43 observers to ensure hassle-free polls, he added.
In Meghalaya, except for the two state parties - the United Democratic Party and the Hills State Peoples Democratic Party - which forged a pre-poll alliance and are contesting in 45 seats, 13 other political parties are contesting independently.
The Congress and BJP are pitted against each other with the former fielding 59 candidates and the latter has put up nominees in 47 constituencies.
Though they are contesting the polls separately, in Meghalaya, the National People's Party (NPP) of Conrad Sangma, son of former Lok Sabha speaker P A Sangma, is BJP's partner in the North East Democratic Alliance (NEDA).
The saffron party is seeking to expand its footprint in the north-east buoyed by the formation of governments in Assam, Manipur and Arunachal Pradesh.