Pirates seized the Mozambique-flagged Vega 5 fishing boat in December and have been using it as their mother vessel since then, CNN reported.
Indian military officials called the capture during the weekend their greatest success in a single anti-piracy operation.
"This vessel had been a risk to international shipping for the last four months and has carried out several attacks," a navy statement said.
A navy plane spotted the ship in the Arabian Sea after pirates on board attempted to hijack another boat Friday. After an exchange of gunfire, Indian patrols captured the pirates, who were suspected to be Somalis.
The Indian navy captured 43 suspected pirates in two other events earlier this year.