The spokesperson for the IMN, Ibrahim Musa, said Mr El-Zakzaky began his return journey to Abuja at 5 p.m. Nigerian time.
A video clip posted on Twitter also showed Mr El-Zakzaky explaining that the Indian hospital had agreed to allow him and his wife Zeenat to come back to Nigeria, following a stalemate over the choice of doctors to attend to them and the terms of treatment.
PREMIUM TIMES reported how the Shiite cleric, two days after arriving at the Medanta Hospital, New Delhi, for medical treatment, cried out over what he described as the pathetic and worrisome situation he had been subjected to at the Indian hospital.
In an audio clip in Hausa language, Mr El-Zakzaky lamented the high-security presence around him in the hospital as well as the refusal of the hospital to allow his personal doctors to supervise his operations.
However, in a swift reaction, the Nigerian government attributed the travails faced by the Shiite leader at the Indian hospital to his actions and violations of terms of travel.
The cleric travelled on Monday following an order of a Kaduna court. He had asked to be allowed to travel to India for treatment for injuries sustained during his arrest in December 2015.
Mr El-Zakzaky and his wife were arrested after soldiers clamped down on the Shiites killing over 300 members of the sect for allegedly blocking a public road.
The cleric and his wife are now being prosecuted by the Kaduna government for their roles in the death of a soldier during the massacre of the Shiite members.