The warning was issued late Wednesday and people have been asked to take precautions and avoid large gatherings since the possibility of contracting the virus is high.
Vikas Desai, head of the preventive social medicine department, said two people - Dipak Tarsariya (24) and Kanji Ghaskata (36), both residents of Katargam area in Surat, died due to the disease.
Desai, however, ruled out the possibility of plague in the city.
"Tests have not revealed any plague symptoms so far. Serum samples collected from the patients have been sent to the New Delhi-based National Institute of Communicable Diseases for further tests," said Desai.
After the weeklong deluge, people began fleeing the city in large numbers fearing epidemics. Memories of the 1994 plague continue to haunt the people of Surat - that took at least 50 lives - and not too many are ready to take any chances.
The rains and flooding in Gujarat has also led to an outbreak of chikungunya across the state, especially in Ahmedabad. Chikungunya is a relatively rare form of viral fever caused by bite of the Aedes aegypti mosquito.
Ahmedabad Municipal Commissioner I.P. Gautam put the figure of such cases at 2,500. He said all 43 urban health centres in the city were assigned the task of distributing chikungunya medicines. Sixty-two mobile dispensaries have also been allocated for the purpose.
The corporation has also set up a special round-the-clock control room, and around 1,000 municipal workers are carrying out a door-to-door survey and awareness campaign.