HNLC spokesman Sainkupar Nongtraw said the shutdown was called in protest against the Indian political leadership and the alleged atrocities perpetrated by the "Sangh Parivar" on minorities.
Shah, who recently visited Mizoram, Nagaland and Manipur, is scheduled to arrive here from Sikkim on April 22 for a day-long visit.
He will address BJP workers and hold series of meetings with leaders of regional political parties, besides holding a separate meeting with church leaders and civil society groups.
Alleging that the BJP was re-writing the constitution for establishing a Hindu state, Nongtraw warned: "If the BJP, RSS, VHP do not stop their religious fanatics policies then the BJP should close down all its party offices in Khasi, Jaintia hills and members of the BJP, candidates contesting elections shall bear the wrath of the HNLC."
However, the BJP's Meghalaya unit has made elaborate arrangements to welcome its national president.
"We have made all necessary arrangements to ensure a successful visit by Shah to Meghalaya. The party president will address party workers and also held separate meetings with the state party office bearers to draw a roadmap for the progress of BJP in Meghalaya," BJP general secretary Dipayan Chakraborty told IANS.
On the other hand, Meghalaya Police said elaborate security arrangement would be made for the BJP national president to ensure his safety and security.
"The police will provide security to Amit Shah as he is a Z-plus protectee and also to ensure his safety and security during his visit in the state," a police officer said.
The HNLC, which runs hit-and-run operations from its hideouts in Bangladesh, has been demanding a sovereign Khasi homeland in Meghalaya.
Meghalaya shares a 443-km border with Bangladesh, part of which is porous, hilly and unfenced and prone to frequent infiltration.