Almost all the government offices located in the 11 district headquarters remained closed.
National Highway Nos.40 and 44, the lifelines for Mizoram, Tripura and parts of Manipur and southern Assam, were affected.
"Attendance in all government offices was very thin in the state capital," principal secretary in-charge of home K.S. Kropha told IANS.
The 13 organisations that called the shutdown include the powerful Khasi Students' Union, the Federation of Khasi, Jaintia and Garo People, and the Hynniewtrep National Youth Front.
Demanding introduction of the ILP system, they say its absence would result in the number of people entering Meghalaya getting out of control, given the state's proximity to Bangladesh and Assam.
Inner Line Permit is an official travel document issued by the central government to allow inward travel of an Indian citizen into a protected/restricted area for a limited period. It is obligatory for Indian citizens not residents of those states to obtain permit for entering into the restricted areas.
However, the Meghalaya assembly had brushed aside a resolution to introduce the ILP to combat influx and illegal immigrants in the state.
Chief Minister Mukul Sangma has promised to enact a stringent law to arrest the influx of illegal immigrants.
"We will enact the Meghalaya Regulation of Landlords and Verification of Tenant Bill, 2013, to regulate the stay of outsiders, especially the 'floating population', in the state to tackle influx and illegal immigration," Sangma said.
Sangma said his government would soon take up with the central government a proposal for appropriate amendment to the Representation of People Act to ensure outsiders in the state do not get voting rights.
The protesting organisations said they would intensify their agitation till the government implements the ILP system.
"The implementation of the ILP would help protect the tribal population from being 'annihilated' in their own land," Joe Marwein, spokesperson of the agitating organisations, said.
--IANS (Posted on 17-10-2013)