Egypt's foreign ministry said it summoned Qatar's ambassador on Saturday to protest Doha's criticism of the military-installed government's crackdown on the Muslim Brotherhood.
Relations between the countries deteriorated with the Egyptian military's overthrow of president Mohamed Morsi and subsequent deadly crackdown on his Muslim Brotherhood movement, which Qatar backs.
Al-Jazeera television, based in Qatar, has also incensed Egypt's government with its coverage of a police crackdown on persistent Brotherhood protests since Morsi's overthrow in July.
"The Qatari ambassador was summoned over a statement by the Qatari foreign ministry," foreign ministry spokesman Badr Abdelatty told AFP.
Late Friday, the Qatari foreign ministry condemned deadly clashes between police and Muslim Brotherhood protesters across Egypt, which killed at least 17 people.
Qatar said it was "concerned by the increase in casualties from the crackdown on protests."
It also criticised Egypt's labelling the Brotherhood last month as a terrorist group, which tightened the screws on the beleaguered movement.
The decision was "a precursor to a shoot-to-kill policy against demonstrators," said the statement, published by the official Qatari QNA news agency.
Doha has backed the Brotherhood in several countries swept by the Arab Spring uprisings of 2011, sparking a backlash from the Islamists' opponents, who accused Qatar of using its natural gas wealth to prop up the organisation.
During Morsi's single year in power, Doha pledged billions of dollars in aid to support Egypt's battered economy, prompting accusations from Morsi's opposition that it was trying to buy influence in the highly nationalistic country.
Doha now harbours several Islamists who fled the crackdown on the Brotherhood following Morsi's overthrow, which killed more than 1,000 people in street clashes and imprisoned thousands more.
Egypt has called on Arab states to respect a 1998 counter-terrorism treaty and hand over Islamists wanted for trial.
One of them is Yousef Qaradawi, a prominent Egyptian-born cleric based in Doha.
Qaradawi faces trial with Morsi and 129 other suspects accused of involvement in jail breaks and attacks on police stations during the early 2011 uprising that toppled strongman Hosni Mubarak.
He rose to prominence through his show on Al-Jazeera, which Egypt accuses of biased coverage of the Brotherhood.
Egypt has jailed several journalists working for the media conglomerate since Morsi's overthrow, including three journalists with Al-Jazeera's English language news operation.
The broadcaster's Cairo bureau chief, Mohammed Fahmy, Australian journalist Peter Greste and producer Baher Mohamed were detained following their arrest last week in a Cairo hotel.
Fahmy has been accused of membership in the "terrorist" Brotherhood, a charge his family denies.
Police had previously raided Al-Jazeera offices in Cairo and confiscated broadcasting equipment.