Baker insisted that Qatar could sustain the impact of what he called a blockade imposed on Doha, but conceded that an impact on profits was inevitable for the Gulf carrier.
"It has to (affect profits) because we have additional costs to operate in and out of the country," he said.
"And this is normal when you are blockading somebody. They will have additional costs to operate in and out of the region."
Last month the airline announced profits of USD 540 million for the financial year to March 2017, a 22 per cent increase on the previous 12-month period.
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But the airline faces a hit after the June 5 decision by Saudi Arabia, the United Arab Emirates, Bahrain and Egypt to impose sanctions on Qatar, over accusations it supports Islamist extremism and was too close to Iran.
Among the sanctions was a decision to close the airspace of the countries to Qatar Airways.
This means the Doha-based carrier can no longer continue its lucrative services to Dubai and Saudi Arabia, and has to divert some flights on longer routes because of airspace restrictions.
Baker said Qatar could endure the crisis for "as long as it is there".
"All the people have a normal life, all the supplies are available, actually more than what it was before, so what is the problem?
"We need our neighbours to know that this kind of bullying doesn't work because the people of Qatar are very robust and we have no issue to have our normal life.
"This is a loss for them not for us."
He was speaking at a ceremony in Doha to show his company's support for Qatari Emir Sheikh Tamim bin Hamad Al- Thani.
The image has become the symbol of the country's defiance during the crisis and Qataris and non-Qataris have queued up to sign the boards expressing their support for the government.