The announcement of the Junagadh Nawab to join Pakistan caused uneasiness among the people of Junagadh and the people opposed the Nawab's action and established an independent provisional government. The Government of India sent a telegram to the Prime Minister of Pakistan, Liaquat Ali, asking him to reject the accession of Junagadh. Lord Mountbatten sent this telegram to Karachi in the hands of the Chief of the Governor General's Staff Lord Ismay. Liaquat Ali refused to accept this demand of the Government of India saying that the telegram sent with Lord Ismay had been refused to be signed by the concerned minister Jawaharlal Nehru. On 13 September 1947, the Government of Pakistan announced that Junagadh Nawab's decision had been accepted and would now be considered a part of Pakistan.
A small contingent from Pakistan was sent to Junagadh by sea. This action of Pakistan was in violation of the agreement reached between the Congress and the Muslim League, in which both sides had agreed that the princely states surrounded by India's borders would have to be found in India.
After Pakistan accepted the announcement of Junagadh annexation, the soldiers of Nawab Muhammad Mahabat Khanji started persecuting the Hindu people of Junagadh State so that the majority of Hindus fled Junagadh. There was a gathering of small Hindu princely states around Junagadh.
The Nawab took over these princely states by sending his armies. He sought help from the Government of India. Mountbatten suggested that the matter should be taken to the United Nations or else a war would break out between India and Pakistan. Sardar Patel did not like this suggestion. They also wanted to challenge Hyderabad and Kashmir by teaching Junagadh a tough lesson.
On 24 September 1947, the Government of India asked the Kathiawar Defense Force to take action against Junagadh. This army surrounded Junagadh from all sides. A few days later, when the Junagadh army lacked logistics, the Indian army moved forward. The people of Junagadh welcomed this army.
On 24 October 1947, the Nawab fled to Pakistan in his special aeroplane. He wanted to take his four wives and hundreds of dogs in an airplane, but one wife and many dogs were left in Junagadh. The Nawab also took all his jewels with him. The Nawab and his family settled in Karachi. On 9 November 1947, the Indian Army captured Junagadh.
On 20 February 1948, a referendum was organized by the Government of India in Junagadh, in which more than 2 lakh population of the princely state participated and 99 percent of the population expressed their desire to join India. Nawab Muhammad Mahabat Khanji died in Pakistan on 17 November 1959. Nawab Shah Nawaz Bhutto of Junagadh also went to Pakistan where he was given a huge land in Karachi.