"The eagles of our nation returned following the successful execution of their tasks," the army said in a statement, referring to the Egyptian air force pilots who carried out the air strikes on militant training camps in the neighbouring country.
The Egyptian Army spokesperson Tamer el-Refae posted a clip on his official Facebook and Twitter pages which included footages of fighter aircraft taking off.
Six air strikes against "terror camps in Libya" were reported by the state-run television.
"The attack resulted in the complete destruction of the targets which included training and concentration areas of [terrorist] elements that participated in the planning and execution of the [Minya] attack," the statement said.
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It said the attack was carried upon the directions of the president and after "coordination and full examination of the information."
The airstrikes came after the Army gathered information that confirms the terrorists' participation in the attack.
The ISIS terror group has claimed responsibility for the attack the Coptic Christians, the second major attack on Egypt's minority community in nearly two months.
In an address to the nation after the attack, President Abdel Fattah al-Sisi said Egypt will not hesitate in striking any camps that harbour or train terrorist elements whether inside Egypt or outside Egypt.
He said the attack will not pass easily.
He said that "all countries that support terrorism, should be punished, without any courtesy or conciliation."
Sisi's remarks came as Trump denounced the attack as "merciless slaughter".
Trump said the US "makes clear to its friends, allies, and partners that the treasured and historic Christian communities of the Middle East must be defended and protected."
"The bloodletting of Christians must end, and all who aid their killers must be punished," he said in a statement.
"We are waging a war on behalf of the world," he said.
Sisi said that recent attacks were aimed at making people believe that Christians are not secure in Egypt, and that the government is not protecting them.
The attack comes as the country is still under a three- month state of emergency period following twin attacks on Coptic churches on Palm Sunday last month that killed dozens of people, in attacks claimed by ISIS.
There have been a number of attacks on Coptic Christians in the country in recent months claimed by Islamic State militants.
On April 9, two suicide bombers hit Saint George's Cathedral in Tanta and St Mark's Cathedral in Alexandria, killing and injuring dozens in the deadliest attack against civilians in the country's recent history. A total of 29 people died in the Tanta explosion and 18 in Alexandria.
In December last year, an attack on a Coptic church in Cairo killed 25 people.
Coptic Christians, which make up about 10 per cent of Egypt's 91 million population, have faced persecution in Egypt, which has spiked since the toppling of Hosni Mubarak's regime in 2011.