In the general elections of 1998, K. R. Narayanan became the first sitting President to vote (16 February 1998), casting his vote at a polling booth in a school within the Rashtrapati Bhavan complex after standing in a queue like an ordinary citizen. He insisted on casting his vote, despite the departure from precedent being pointed out to him. Narayanan sought to change what was a long-standing practice of Indian presidents not voting during general elections. He also exercised his franchise as President in the 1999 general elections.
One of the coalition partners supporting the minority government (the All India Anna Dravida Munnetra Kazhagam under J. Jayalalithaa) wrote a letter to the President withdrawing support on 14 April 1999, and Narayanan advised Vajpayee to seek a vote of confidence in the Lok Sabha. This motion was defeated (17 April). Both Vajpayee and the Leader of the Opposition, Congress president Sonia Gandhi, then staked claims to form the government. Narayanan asked the NDA and the Congress party to show proof of support since the loss of the confidence vote. When evidence from neither party was forthcoming, Narayanan informed the Prime minister that fresh elections seemed to be the only way to resolve the crisis in governance. The Lok Sabha was then dissolved at Vajpayee's advice (26 April). (In the ensuing general elections, the NDA secured a majority and Vajpayee was reappointed Prime minister (11 October 1999) in a straightforward manner.)
President Narayanan returned for reconsideration the advices from the Union cabinet to impose President's rule in a state, in accordance with Article 356, in two instances: one from the Gujral government (22 October 1997) seeking to dismiss the Kalyan Singh government in Uttar Pradesh, and the other from the Vajpayee government (25 September 1998) seeking to dismiss the Rabri Devi government in Bihar. In both instances, he cited the Supreme court judgement of 1994 on S. R. Bommai vs. Union of India and exercised his discretion by, in the former case, returning the matter for reconsideration of the cabinet, which then decided not to move ahead in the matter. However, in the latter case, the cabinet re-advised the same to the president after couple of months, It was then the President's rule was imposed in Bihar in February, 1999.
A military conflict was developed in Kargil on the Line of Control (LoC) with Pakistan in May 1999. The Vajpayee government had lost a no-confidence vote in Lok Sabha earlier that year and the opposition failed to form the next government. The Lok Sabha had been dissolved and a caretaker government was in office. This caused a problem with democratic accountability, as every major government decision is expected to be discussed, deliberated and consented by the parliament. Narayanan suggested to Vajpayee that the Rajya Sabha be convened to discuss the conflict, as demanded by several opposition parties (citing the precedent of Nehru convening a parliamentary session on Vajpayee's demand during the Sino-Indian war in 1962 ) though there was no precedent of convening the Rajya Sabha in isolation during an interregnum. Further, Narayanan was briefed by the chiefs of the three arms of the Indian Armed Forces on the conduct of the conflict. His Republic day address next year began by paying homage to the soldiers who had died defending the nation.