He was accompanied by a team of Karnataka Police officials.
Earlier, he was not allowed to board a flight at the airport in Bengaluru here on security grounds by IndiGo airlines.
However, later the airlines allowed him to board in their flight.
A rousing welcome was accorded to Madani by his supporters, who were waiting for his arrival since morning outside the Kochi international airport at Nedumbassery.
"I am grateful to Almighty for granting me an opportunity to celebrate Holy Ramadan with people of Kerala and my parents after six long years," he said.
Madani also thanked the people of Kerala and media for extending their support to him at a time when he was undergoing a period in which he was "denied justice."
He, however, refused to say anything on the case against him in Karnataka.
A special National Investigation Agencycourt based on the Supreme Court directions had recently fixed thedate for his travel to Kochi from Bengaluru from July 4 to July 12.
It had directed the city police to provide necessary security arrangements.
Earlier in Kochi, supporters of Madani staged a violent
protest outside the airport and allegedly smashed glass at the counter of Indigo for allegedly refusing to carry their leader to Kochi from Bengaluru.
Police used force to push out around slogan shouting supporters of the jailed leader from the domestic departure area of the terminal building sensing that their protest was turning a big security threat for the airport, police said.
According to Kerala Police, around 500 supporters of Madani had gathered outside the terminal to receive the PDP leader on his arrival by the Indigo flight at noon.
They ended their protest after they got an assurance that Madani will reach by air in the night.
Earlier, listing out the instructions to be strictly adhered to by all concerned for carriage of person under judicial custody/ administrative control as per the Bureau of Civil Aviation Security (BCAS) regulations, IndiGo had said in Bengaluru that as an airline, it always complies with the security agencies regulations.
Also, it stipulates that a minimum of two escorts of the policing authority shall be required for one prisoner who is classified as dangerous by the policing authority.
It also noted that aircraft operator should not accept a prisoner and escort(s) as passengers unless concurrence has been obtained in advance from the BCAS and other operators that may be involved en route and at the intended final destination.
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