In 1949, more than 8 lakh refugees entered West Bengal, Assam and Tripura from East Pakistan. These refugees were being forced into Indian territories by Pakistani authorities. These were Hindu citizens killed by violence and persecution. Nehru invited the Prime Minister of Pakistan Liaquat Ali Khan to find a peaceful solution to this problem. Dissatisfied with Nehru's manner, Patel met Liaquat Ali Khan and sent him a message in a stern tone that he should desist from such antics.
On this, Nehru proposed to Liaquat Ali Khan that both India and Pakistan should establish minority commissions. Patel strongly criticized this proposal of Nehru. Shyama Prasad Mukherjee and K. C. Negi, angry with Nehru's policies of appeasement, resigned from the cabinet.