The 48-year-old president of the Board of Control for Cricket in India (BCCI) is "responding well to treatment", the body's secretary Jay Shah said.
He developed chest pains while exercising and has now had surgery.
Ganguly played 113 Tests and 311 one-day internationals, captaining India in the longest format 49 times between 2000 and 2005.
Doctors said Ganguly had an angioplasty - a procedure to unblock a coronary artery - in hospital in Kolkata and would be monitored for 24 hours.
A left-handed batsman, Ganguly scored 7,212 Test runs and scored 16 centuries.
He is ninth on the all-time ODI run-scorers list with 11,363. He scored 22 hundreds in the 50-over format.
He took over as president of the Indian cricket board in October 2019.
India captain Virat Kohli tweeted: "Praying for your speedy recovery. Get well soon."
Photo Getty Images Caption: Former India captain Sourav Ganguly