"The health of Sheikh Zakzaky and his wife, Malama Zeenatudeen, is deteriorating. They are suffering from various health complications with gun injuries on their bodies since 2015," Mahdi Garba, a member of the Shia movement, told Al Jazeera.
He left for India from Abuja's international airport.
In recent weeks, IMN members had carried out a series of demonstrations in the Nigerian capital, demanding the release of el Zakzaky.
El Zakzaky and his wife had been held in a detention facility since December 2015.
In 2016, a court said that el-Zakzaky should be released but authorities refused and have since filed charges against him including homicide, unlawful assembly, disruption of public peace and other offences.