It long has denied supporting militant groups and described the crisis as being fuelled by "absolute fabrications" stemming from a recent hack of its state-run news agency.
The Gulf states and Egypt banned all flights to and from Qatar and ordered Qatari citizens to leave within 14 days.
Asked about the reasons standing behind the crisis sheikh Mohammed said "We do not know exactly what are the real reasons for the current crisis", and if there were real reasons so why all these media propaganda are targeting Qatar and its sovereignty.More news: Latest Stocks: AmTrust Financial Services Inc (AFSI) Downgraded by TheStreet to C
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Flight tracker websites showed Qatar Airways flights taking a circuitous route mostly over Iran to avoid their neighbours. Some of its flights were going through Iranian airspace Monday.
Qatar Airways, for its part, said it had suspended all flights to Saudi Arabia, the UAE, Bahrain and Egypt "until further notice".
"The Qatari Government will take all necessary measures to ensure this and to thwart attempts to influence and harm the Qatari society and economy", it said.
UAE carriers Emirates, Etihad, flydubai and Air Arabia, as well as Saudi Airlines had all announced the suspension of flights to and from Qatar as of Tuesday morning. But Gulf Arab neighbours and Egypt have always been irked by its maverick stances and support for the Muslim Brotherhood, which they regard as a political enemy.
Qatar is home to the forward headquarters of the US military's Central Command.