Dr. Waldemar Mordecai Haffkine, a Russian scientist, and a student of the great Louis Pasteur had arrived in India in March 1893, and was fighting a lone battle against Cholera in Calcutta by inoculating the population with the Cholera vaccine developed by him in Paris. This work evoked so much interest that in 1896, when an epidemic of plague broke out in Bombay and Poona, the then Governor of Bombay invited Dr. W M Haffkine to Bombay and provided some laboratory space to him on the campus of JJ Group of Hospitals to work on plague vaccine. Dr. Haffkine accepted the challenge and successfully developed the plague vaccine, and on January10, 1897, he vaccinated himself to test the safety of his vaccine.

On the 10th of August 1899, the present mansion, which was at one time the residence of the Governor of Bombay, was formally handed over to Dr. W M Haffkine by the Governor Lord Sandhurst.

This present building in which Dr. Haffkine worked has an interesting story. It is supposed to have been built on the site of an old temple of Parli Vaijnath, which gave the name Parel to the adjoining village. On this site the Jesuits built a Monastery and the Chapel sometime between 1596-1693. The exact date is not known, but the present premise of Haffkine Institute was known as Romish Chapel of Jesuits and was in existence in 1673. The Chapel had extensive grounds of its own almost resembling a park with big spreading trees growing all over. From the estates in Bombay, Jesuits maintained a Mission in Agra and Japan, even when Bombay had passed into the hands of the British because according to the Treaty of 1665, the Portuguese were not to be interfered with in their religious order. In the year 1719, the British confiscated all Jesuit properties after a Maratha invasion, on the plea that the Jesuits had allowed the Marathas to mount their guns aimed at the British from one of their properties at Bandra.The building, thereafter, became the residence of Registrars of Bombay until the demolition of the Fort. The Governors of Bombay used to live in Parel after leaving the Fort. The building was then known as Government House. This area was then considered to be a very aristocratic locality. In 1885, the Governors left this residence and the premises were used as House of Recorders of the Bombay Presidency. In 1895, King Edward VII visited India as Prince of Wales, and stayed on the premises for a week. On such a historical premises Dr.Haffkine entered on 10th August 1899. At that time it was designated as "Plague Research Laboratory" with Dr. W M Haffkine as its Director in Chief. In 1906 the Institute was renamed as "Bombay Bacteriology Laboratory". Finally, in 1925, due to the efforts of Lt. Col. F.P. Mackie, the Institute was aptly named as "Haffkine Institute". By the time Dr. Haffkine left India in 1904, the Institute had developed the technology for the production of plague and cholera vaccines. The Institute advanced continuously, inheriting the spirit of challenge of the founder Director, Dr. Haffkine. New disciplines were pursued and newer departments were established.