Saudi Arabia, the United Arab Emirates and Bahrain have said they are withdrawing their ambassadors from Qatar because Doha had not implemented an agreement among Gulf Arab countries not to interfere in each others' internal affairs.
The three countries said the move was necessary "to protect their security and stability".
According to a report published by Saudi state media on Wednesday, the decision to withdraw diplomatic envoys was made because Qatar did not implement a security pact about non-interference in the internal affairs of the other states that make up the Gulf Cooperation Council (GCC).
A joint statement from the three countries claimed Qatar failed to commit "to the principles" of the GCC.
A security agreement signed last year by the GCC focused on co-operation in the exchange of information and tracking down of criminals and those who broke the law.
Qatar's government said it expressed "disappointment and surprise at the statement issued by the brotherly countries".
"The moves taken by the Kingdom of Saudi Arabia, UAE and Bahrain have nothing to do with their national interests nor their security and stability, but there is a difference of opinion and position on a number of issues outside the Gulf Co-operation Council."
The statement further said that Qatar was committed to "brotherly principles concerning their brothers in the council".
In an interview with Al Jazeera, Nasser bin Hamad Al Khalifa, the former Qatar ambassador to the UN and US, called the decision "a big mistake".
"It is unfortunate that some of them [GCC countries] are trying to force Qatar to take certain policies which have nothing to do with the Gulf, nothing to do with Saudi Arabia or the United Arab Emirates or Bahrain."
"The whole issue is really about Sisi," he said, referring to the Egyptian general Abdel Fattah el-Sisi, who removed Mohamed Morsi from the presidency last year.
"These countries, they are supporting a coup d'etat where thousands of Egyptians are being killed in front of the whole world. And they want Qatar to support such a policy," Khalifa said.
"But we will never support any regime which kills its own people."
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"I am sure in the days after that wisdom will come and these countries will realise that trying to impose the philosophy of my way and the highway will not work with Qatar," Khalifa said.
The joint statement said GCC members had signed an agreement on November 23 not to back "anyone threatening the security and stability of the GCC whether as groups or individuals - via direct security work or through political influence, and not to support hostile media."
GCC foreign ministers had met in Riyadh on Tuesday to try to persuade Qatar to implement the agreement, it said.
"But unfortunately, these efforts did not result in Qatar's agreement to abide by these measures, which prompted the three countries to start what they saw as necessary, to protect their security and stability, by withdrawing their ambassadors from Qatar starting from today, March 5 2014," the statement said.
The move is thought to be unprecedented in the three-decade history of the GCC, a pro-Western alliance of Saudi Arabia, Bahrain, Kuwait, Qatar, UAE and Oman.
The Qatar stock exchange closed 2.09 percent down following the decision.