Leader of the Islamic Movement in Nigeria (IMN) Sheikh Ibrahim Zakzaky has left India after rejecting the Nigerian government's "obstruction" of his medical treatment.

Speaking to the AFP on Friday, Zakzaky's daughter Suhailah Zakzaky confirmed that Zakzaky had left New Delhi for Nigeria. "They did fly with Ethiopian Airlines," she said.

Zakzaky returned along with his wife Mallimah Zinat -- who was also seeking treatment for injuries -- after announcing his planned departure earlier on Thursday.

The London-based Islamic Human Rights Commission, a non-profit organization, said the couple had “lost all faith” in the prospect of receiving proper treatment in India.

The top Muslim cleric and his wife were injured in a deadly military raid in 2015. They had been in prison until last week for four years despite a high court ruling granting them freedom.

The IMN published a statement on Thursday confirming the departure.

"The Nigerian government’s interference and scuttling of the whole process rather than supervision as ordered by the court is the direct cause of the impasse," it said.

"The Islamic Movement is completely not happy with the latest development, and we strongly believe any peace-loving person in Nigeria feels the same. The government left no one in doubt that it never wanted the Sheikh to go for the medical treatment in the first place," the statement added.

The house of the 66-year-old cleric, who is the leader of the Islamic Movement in Nigeria (IMN), was raided in 2015 after the Nigerian government alleged that his supporters had blocked a convoy of the country’s defense minister. The movement has categorically rejected the allegation.

During the raid, Sheikh Zakzaky was beaten and lost his left eye. His wife sustained serious wounds, and three of his sons and more than 300 of his followers were killed.

The couple were put in custody afterwards. A Nigerian court granted the Muslim cleric bail last week so that he could fly to India for treatment.