The three countries' aviation bodies also said that non-Qatari private and chartered flights from Qatar must submit requests to them at least 24 hours before crossing the airspace.
Saudi Arabia and its Gulf allies accuse Qatar of supporting "terrorism" in the region, something Doha denies, while Doha's supporters - such as Turkey - have warned of a humanitarian crisis.
A senior counter-terrorism adviser to Qatar's foreign minister has hit out at the diplomatic squeeze on Doha by several Gulf states, calling it a "policy of domination and control".
Addressing lawmakers of the ruling Justice and Development Party in Ankara, Erdogan said "depriving Qatari people from food and water, travel, or worship is inhumane, non-Islamic".
The most visible member of the government has been Sheikh Mohammed, who has said Qatar would not "surrender" to the political pressure.
Qatar is facing restricted airspace access since the diplomatic curtain fell around its borders. That helped spark the crisis, which began June 5 when Saudi Arabia, the UAE, Bahrain and Egypt cut diplomatic ties and started trying to isolate Qatar from the rest of the world.
As a result Qatar's only land border has been closed, it has been stopped from using the airspace of neighbouring nations, and its citizens have been told to leave various Gulf countries within two weeks.
The proposal - described as the biggest airlift of cattle ever attempted - comes as Qatar moves rapidly to open an air and sea bridge via Iran, Turkey and port facilities in Oman. Qatar's close relationship with the Islamic Republic is one of the factors believed to be behind the rift.
But Emadi said the energy sector and economy of the world's top liquefied natural gas exporter were essentially operating as normal and that there had not been a serious impact on supplies of food or other goods.
In his strongest comments yet on the crisis, Erdogan added that Qatar was a country "on which a death sentenced had in some way been pronounced".
Earlier, Turkish Foreign Minister Mevlut Cavusoglu said that Erdogan would hold talks on the crisis with Trump in the coming days.
"Dialogue should be continued under all circumstances so the existing problems can be solved in a peaceful way", he said, according to Turkish state news agency Anadolu last week. "Victimising Qatar through smear campaigns serves no objective", he said during a parliamentary address, using the Arabic abbreviation for the Islamic State of Iraq and the Levant (ISIL, also known as ISIS), on Tuesday.