"The decision was taken due to the political position of Qatar vis-s-vis Egypt since the revolution of June 30, 2013," federation head Yasser Idriss explained.
Mass demonstrations led to the ousting of Egypt's Islamist president Mohamed Morsi in July last year.
Relations between Egypt and Qatar soured after Morsi's ouster, as Cairo criticised Doha's backing for the former head of the state's Muslim Brotherhood.
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Over 1,400 pro-Morsi supporters have been killed and 15,000 detained since he was deposed.
Idriss said that the Egyptian swimming federation was prepared to accept any punishment for its decision not to compete in the championships scheduled from December 3 to 7.
The boycott he revealed was voted on by the federation's board without the Egyptian Sports minister being consulted.
This protest by the Egyptian swimmers comes as Egypt's men's handball team is due to compete in the 2015 handball world championships also in Qatar starting on January 15.
The United Arab Emirates and Bahrain have already pulled out of the event in apparent protest at Qatar's backing for Islamist groups in the region.