A total of 4,580 Katsina State pilgrims have so far been transported to Saudi Arabia for the 2017 Hajj.
"Limiting the transfer of Qatari pilgrims to Saudi Arabian Airlines is unprecedented, illogical, surprising and contravenes the teachings of Islam", Xinhau news agency quoted Ahmed bin Saeed Al-Rumaihi, the ministry's information office director, as saying in a statement. In 2016, about 1.8 million pilgrims performed hajj.
The Emirates' Senior Vice-President, Commercial Operations, Gulf, Middle East and Iran, Adil Al Ghaith, said that travelling for hajj was a unique experience for Muslims around the world, and the airline expected over 20,000 pilgrims to travel with it this year.
Qatar has denied the allegations.
"Qatar to oversee its haj contingent and the transportation of Qatari pilgrims via their choice of airlines, Qatar Airways or otherwise", he added.
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Saudi Arabian Airlines on Sunday said Qatari authorities had refused to grant a Saudi Arabian Airlines flight, scheduled to transport Qatari hajj pilgrims, permission to land at Hamad International Airport.
Saudi Arabia, together with the UAE, Bahrain and Egypt, cut diplomatic ties with Qatar and imposed a full blockade on it in June, citing Doha's support for terrorism and interfering in the domestic affairs of its neighbours.
Last week, Saudi Arabia unilaterally reopened its border with Qatar to allow Qataris to attend the hajj amid a monthslong rift between the neighboring countries.
The Saudi-led embargo has had an economic impact on Qatar.