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US Secretary of State Mike Pompeo praised Egypt President Abdel Fattah al-Sisi and the country's "religious freedom" during a visit on Thursday, despite a massive regime crackdown on pro-democracy activists.

Pompeo visited a huge cathedral and mosque in the country's new capital east of Cairo on Thursday, as part of a major tour of the Middle East, which has already seen him stop at Jordan and Iraq.

Pompeo describes himself as an evangelical Christian, and on Thursday evening he visited the Cathedral of the Nativity of Christ in Egypt's New Administrative Capital, 45 kilometres (28 miles) east of the capital.

He also visited the al-Fattah al-Alim mega-mosque, where he praised Egypt's "freedoms here in this houses of worship, these big, beautiful, gorgeous buildings where the Lord is clearly at work".

The two buildings were inaugurated by President Abdel Fattah al-Sisi on Sunday, a day after a deadly bomb blast near a church.

Asked about the role of governments towards religious minorities, Pompeo said Cairo had "an obligation to make sure that every individual can choose to worship the way they want or choose".

"It's wonderful that here in Egypt it's possible," he said.

Islamic State group militants have repeatedly targeted Egyptian-Christians, with 128 Christians killed and 200 driven from their homes due to their faith in 2017, according to the Open Doors charity.

Pompeo praised Sisi during his visit for his public acknowledgement of Christianity in the country with the new cathedral.

Egypt's some 10 million Christians - around ten percent of the population - still face discrimination in the country but this did not stop Pompeo praising Sisi for Egypt's alleged religious pluralism.

"This is a special country where President Sisi clearly made a point by putting this, this largest cathedral in the Middle East here in this place," Pompeo said, calling the building "a great symbol of hope". 

US President Donald Trump wrote on Twitter that he was "excited to see our friends in Egypt opening the biggest Cathedral in the Middle East".

"Sisi is moving his country to a more inclusive future."

Sisi, a former army chief, led a  Islamist president Mohamed Morsi, is accused of leading a massive crackdown on both human rights activists and Islamists, which has seen tens of thousands detained.

Agencies contributed to this story.