A foreign ministry official said Doha was recalling its envoy over a statement made by Egypt's delegate to the Arab League Tariq Adel, according to the QNA state news agency.
Adel accused Qatar of supporting terrorism, according to Egyptian media and the Al-Jazeera news channel, after Doha's representative expressed reservations over a clause in a communique welcoming Cairo's air strikes on Islamic State targets.
The communique was released at the end of an ambassador-level Arab League meeting in the Egyptian capital.
In a separate release, Qatar's foreign ministry said Doha had expressed reservations over welcoming the raids, stressing the need for "consultations before any unilateral military action against another member state."
It denounced the "tense" statement by Egypt's representative to the Arab League, saying it "confuses the need to combat terrorism (with)... The brutal killing and burning of civilians.