The media accused Patel that his home ministry could not protect Gandhi. Saddened by this, Patel resigned from the government. To this, Nehru rejected Patel's resignation saying that Nehru and Patel had been working together in the Congress for thirty years for a common cause and it would not be a good thing for both of them to fight after Gandhi's death. Patel's resignation was averted, but even after that, differences remained between Nehru and Patel on political issues. Sharp differences between Patel and Nehru over the three policies adopted by Nehru - taking the Kashmir issue to the United Nations in 1948, not giving aid to Tibet against China in 1950 and not taking military action to expel the Portuguese from Goa, Patel remained till his death. When Nehru tried to sideline Patel and the Home Ministry officials on the Kashmir issue, Patel reacted strongly.
In 1950, Nehru pressurized Dr. Rajendra Prasad to withdraw his presidential nomination in favor of Rajagopalachari. This action of Nehru deeply angered the Congress leaders. The Congressmen felt that Nehru was trying to impose his will on the Congress. Nehru asked Patel to help Nehru in getting Rajagopalachari as the President. On this, Patel refused to work against the wishes of the party and Dr. Rajendra Prasad was made the first President of India. In 1950, Nehru stood for the post of President of Congress Purushottam Das Tandon. Tandon's image was that of a Hindu leader, so Nehru opposed him and appealed to make Jeevram Kriplani the President of Congress, saying that if this does not happen then Nehru will resign. Patel opposed Nehru's approach and announced his support to Tandon in Gujarat. Kripalani was a resident of Gujarat but he did not get a single vote from Gujarat. Patel believed that Nehru's wish was not the law for the Congress, but when Tandon won, Nehru understood that he had lost all the confidence of the Congress. On this Nehru resigned from his post. Then Patel refused to resign Nehru.