The primary cause for this was India's preoccupation with Indo-Muslim solidarity. Most attribute this solidarity to two causes: (1) making common cause with the anti-colonial "Non-Aligned Movement", which was convinced that Israel was a colonial project and which involved numerous Arab states India sought to work with; and (2) fear that any other policy might anger India's substantial Muslim minority. Both of these policy rationales were used during the Cold War to justify India's refusal to upgrade relations with Israel, which obviously changed following the end of the Cold War and the diminishing importance of the Non-Aligned Movement. India began to see upsides to establishing relations with Israel, including improving relations with the United States (the "victor" of the Cold War) as well as a calculation that the Arab states had not yielded many benefits to India as allies. India supposed that Israel's close connection with the United States could give it a "foot in the door" with ties to the United States, particularly now that the Cold War had ended, and also saw that no Arab state had made significant moves towards supporting India in the Indo-Pakistani conflict, which meant Indian strategic goals benefited little from the Arab alliance. Furthermore, the BJP-led coalition in 1998 had long argued these points, and chose to continue expanding relations with Israel along these lines.

India also had a conflicted view on the Jewish state's establishment, in part due to Gandhi's conflicted views on Jewish nationalism. He did not believe in a religious state or a mandated one, which was how many viewed Israel in its early years, and which likely affected the decision to vote against partition in 1947 and also against Israel's admission to the United Nations in 1949. Upon recognizing Israel in 1950, Indian Prime Minister Nehru said quite clearly that India had until then "refrained because of our desire not to offend the sentiments of our friends in the Arab countries". This ensured India kept a steady flow of oil from the Arab world (more or less), and also was important to the Indian economy's thousands of workers in the Gulf states, which helped India's foreign exchange reserves over time as well. These factors, from the ideological association of Israel with Pakistan in Indian thought (as a "religious" state, despite their differences), the desire for closeness with the Arab world, the attempt to make inroads among the Muslim world against Pakistani influence, and the desire to stay part of the NAM during the Cold War, came together to make Israel a state India would only work with in clandestine fashion at best, which occurred quite often during India's wars with China and Pakistan. Israel's intelligence services provided India with support in the 1962 and 1965 wars, respectively, though following the 1967 war, the clandestine agreements on security bases between the two states took a nosedive due to the worsening of the Arab-Israeli conflict.