The outlawed Hynniewtrep National Liberation Council (HNLC) has called for a 36-hour shutdown - starting 6 a.m. Monday to protest against Mukherjee's two-day visit to Shillong, the capital of Meghalaya.
Police and para-military personnel have been posted on all major thoroughfares and patrolling has been intensified throughout the state, officials said.
Chief Secretary WMS Pariat reviewed the security scenario.
A government statement said, "While steps are being taken to provide all necessary security arrangements for the protection of all sections of the people, the government appeals to each and every citizen to come out to greet the President on this auspicious occasion.
"This will be an indication of our maturity and send out a strong message that people of the state can no longer be held to siege at every turn," it stated.
Governor KK Paul and chief minister Mukul Sangma will receive Mukherjee at the Advanced Landing Ground in Shillong.
The President will address the state assembly and visit the Brookside bungalow at Rilbong where Nobel laureate Rabindranath Tagore had stayed during his visit in 1919.
He will also visit the Don Bosco Museum, Asia's largest museum for the indigenous cultures of the north-east.
The President will confer degrees on the students during its 21st convocation.
The President, who is also the Visitor of the North Eastern Hill University, will confer degrees on the students during its 21st convocation Oct 22 before returning to Delhi.
The Informed Conscious and Responsible Existence (ICARE), an intellectuals group, will organise a public gathering Monday morning at Khyndailad in Shillong to protest against the 36-hour HNLC shutdown.
The HNLC, which runs hit-and-run operations from its hideout 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.