The SIT has been constituted and has been directed to complete the probe within a month, Shah said.
Modi called on the people of the state to vote for the BJP-NDPP alliance 'which would ensure that the funds reach the people'.
Adequate security and Covid safety measures have been put in place for the electoral exercise.
The Bharatiya Janata Party and Congress on Sunday were set to share the honours in the Lok Sabha and assembly bye-elections in 13 states.
Buoyed by the formation of governments in Assam, Manipur and Arunachal Pradesh, the BJP is making a bid to expand its footprints in the region.
The counting will begin at 8 am, and as per the Election Commission's COVID-19 guidelines, a candidate, his poll agent and counting agent can remain present in the counting hall, officials said, adding various measures have been taken to ensure social distancing and avoid crowding.
The venue holds significance as the announcement of Nagaland's statehood on December 1, 1963 was made from Kohima by the then president Sarvepalli Radhakrishnan.
Nagaland Chief Electoral Officer Abhijit Sinha said the violence in Akuluto constituency in Zunheboto district left one dead and two injured.
A close finish is predicted in Meghalaya.
Extensive arrangements have been made due to the COVID-19 pandemic including personal protective equipment kits for election staff, more polling booths, thermal screening, sanitisers, masks and gloves for voters and markings to ensure social distancing, officials said.
Polling will be held between 7 am and 4 pm, except in some polling stations of the interior districts of Nagaland, where the process is scheduled to conclude at 3 pm. The two states have a 60-member House each, but voting will be held for 59 constituencies in both.
Prime Minister Narendra Modi urged people to vote in large numbers. "Today, there are bypolls taking place in various places across India. I urge those voting in these seats to vote in large numbers and strengthen the festival of democracy," he said in a tweet.
Parliament's monsoon session began amid sloganeering and protests from opposition of different issues.
'Had the BJP gone along with the NPP, that would have eased the task of the Congress of winning more seats.' 'That was a great strategy of the BJP.' 'It helped the NPP get more seats than perhaps if it had gone as a pre-alliance partner with the BJP.'
The opposition parties snatched the high-profile Kairana LS seat in from BJP with a united force.
Congress had a reason to smile as it was able to emerge as the single largest party in Meghalaya, but failed to secure a majority.
'The BJP capitalised on the Left Front's failure and inaction and the Congress' deliberate retreat in Tripura.'
Allegations of electronic voting machines malfunctioningreturned to haunt the Election Commission as four Lok Sabha seats and nine assembly constituencies went for bypolls on Monday across 10 states with moderate-to-heavy voting amid prestige at stake for the Bharatiya Janata Party as well as opposition parties ahead of the 2019 general elections.