Qatar, which will host the 2022 FIFA World Cup and is home to some 10,000 American troops, criticized the move as a "violation of its sovereignty".
Gulf Arab states and Egypt have long resented Qatar's support for Islamists, especially the Muslim Brotherhood which they regard as a risky political enemy.
Al Jazeera, in a web-statement, said the reports were false despite being carried on Qatar's official news platform, the Qatar News Agency.
Qatar backed Morsi, in a dispute that led Bahrain, Saudi Arabia and the UAE to withdraw their ambassadors from Doha for several months in 2014.
Al-Jazeera reported that trucks carrying food for Qatar were lining up across the border in Saudi Arabia, unable to enter the country. As India takes over 90 per cent of its natural gas import from Qatar.
As the row deepened, Qatar's Stock Exchange fell by more than 7% - and there has also been volatility with oil prices.
They claim Qatar is funding militant groups which operate in their countries, such as Al-Qaeda, the Muslim Brotherhood and the so-called Islamic State, which Qatar denies.
Qatar had no immediate comment. Some of its flights were going through Iranian airspace Monday. Qatari nationals will be banned from entering the UAE, while Qataris in UAE were given two weeks to leave.
He encouraged Qatar and its neighbours to "sit down together", adding that Washington was ready for "any role that we can play" in helping to overcome divisions.
Turkey, which enjoys friendly relations with Qatar and other Gulf countries, offered its help, with Foreign Minister Mevlut Cavusoglu telling reporters: "We will give any kind of support for the situation to be normalised". Qatar said its state-run news agency and Twitter account were hacked and the story was fake, but state-linked media continued to publish the comments.
Vijayan also made a request that the Indian Embassy in Doha may be suitably empowered to respond presciently to the concerns of the Indian population in Qatar.
Though sources in the airline maintained that flights to Kerala on Tuesday would be operated as per schedule, uncertainty prevails over the travel of Keralites to Gulf states like the United Arab Emirates, Saudi Arabia, Bahrain, Yemen, and Egypt.
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