The diplomatic row came just two months after a thaw began in relations between the two.
Egyptian jets bombed sites in Libya on Monday hours after Islamic State militants there released a video showing the beheading of 21 Egyptian Christians, drawing Cairo directly into the conflict across its border.
Qatar expressed reservations over the attack at a subsequent meeting of the Arab League, angering Cairo.
Saad bin Ali al-Muhannadi, a Qatari foreign ministry official, cited misgivings on “unilateral military action in another member (state) in a way that could harm innocent civilians”.
Despite Qatar’s concerns, the Arab League put out a statement on Wednesday expressing its “complete understanding” over Egypt’s air strikes and threw its weight behind Cairo’s call for a lifting of the arms embargo on the Libyan army.
Qatar also expressed reservations on this point. Al-Muhannadi said it would give leverage to one party over the other before peace talks were concluded and a coalition government was formed.
The Egyptian envoy to the League, Tareq Adel, blasted the moves, saying it shows Qatar “supports terrorism,” according to Egyptian news agency MENA.
But the Western-allied and oil-rich Gulf Cooperation Council sided with Qatar, suggesting it did not want to revive an internal rift which peaked when Saudi Arabia, the United Arab Emirates and Bahrain withdrew their ambassadors from Doha last year over its support for Islamists.
“These accusations are baseless, distort the truth and ignore the sincere efforts Qatar has exerted with its GCC neighbors to combat terrorism and extremism on all its levels,” GCC head Abdullatif Al-Zayani said in a statement.
Egypt, the Arab world’s most populous country, accuses Qatar of supporting the Muslim Brotherhood, which was ousted from power in 2013 when the army moved against President Mohamed Mursi following mass protests against his one-year rule.
Egypt in November heeded an appeal by Saudi Arabia to back an agreement that ended the eight-month spat among Gulf Arab states. That row was over Qatar’s support for the Muslim Brotherhood, which had been designated by several Arab countries as a terrorist organization, and the promotion of Arab Spring revolts.
Egyptian President Abdel Fattah al-Sisi has been keen to please Qatar’s wealthy Gulf neighbors — key financial and political backers of his military-backed government — and may seek to defuse tensions now that the Gulf has expressed its solidarity with the gas-rich kingdom.
Qatari Foreign Minister Khaled al-Attiya, in an interview with the pan-Arab al-Hayat newspaper published on Thursday, said Doha did not support the Muslim Brotherhood, adding that the rift that had divided Gulf Arab nations was history.
Attiya said that there were “differences of opinion, which is healthy, and not disputes” between Gulf Arab countries.