US President Donald Trump has moved to reset relations with Egyptian President Abdel Fattah al-Sisi after the Obama administration's strained ties, giving him firm backing and vowing to work together to fight Islamic militants.

Key points: Mr Sisi's human rights record was a matter of concern in the Obama administration

Mr Sisi's human rights record was a matter of concern in the Obama administration Australian journalist Peter Greste was arrested and tried in Mr Sisi's protester crackdown

Australian journalist Peter Greste was arrested and tried in Mr Sisi's protester crackdown Mr Trump's appraisal marks a shift in tone in US foreign policy with regards to human rights

Mr Trump's appraisal marks a shift in tone in US foreign policy with regards to human rights Rights groups slam Mr Trump's open-armed welcome of Mr Sisi

"I just want to let everybody know in case there was any doubt that we are very much behind President Sisi," Mr Trump said during an Oval Office meeting with the Egyptian leader.

"He's done a fantastic job in a very difficult situation. We are very much behind Egypt and the people of Egypt."

Loading

The trip was Mr Sisi's first official US visit since being elected President in 2014 — Mr Trump's predecessor Barack Obama never extended an invitation citing concern over Mr Sisi's human rights record.

Mr Obama froze aid to Egypt for two years after Mr Sisi — then the country's leading general — overthrew president Mohamed Morsi in mid-2013 after mass protests against Mr Morsi's rule.

Sorry, this video has expired Beverley O'Connor speaks to Sharif Kouddous from The Nation Institute

Mr Morsi, a member of the Muslim Brotherhood, had been democratically elected the previous year.

Human rights groups have estimated that Mr Sisi's government has detained at least 40,000 political prisoners and oversaw the killing of some 1,000 anti-Sisi protesters in August 2013, effectively shutting down the country's Arab Spring movement.

Mr Sisi's government also presided over the arrest and trial of Australian journalist Peter Greste and his two Al Jazeera colleagues.

Human Rights Watch's executive director Kenneth Roth slammed Mr Trump's open-armed welcoming of the controversial Egyptian president.

"Sisi killed 817+ at Rabaa, tortures many, detains 10,000s, but Trump says he has 'a great friend & ally in the US'," he wrote on Twitter.

US, Egypt disagree on 'a few things': Trump

The one-on-one meeting between Mr Trump and Mr Sisi, followed by a separate gathering with top aides, showed how intent the new US President is on rebooting the bilateral relationship and building on the strong connection the two presidents established when they first met in New York last September.

"I just want to say to, Mr President, that you have a great friend and ally in the United States, and in me," Mr Trump said.

Mr Sisi said he appreciated that Mr Trump has been "standing very strong ... to counter this evil ideology".

Loading

While Mr Trump noted the United States and Egypt "have a few things" they do not agree on, he made no public airing of US concerns about human rights in Egypt.

However at the United Nations in New York, US ambassador to the United Nations, Nikki Haley, said the Trump administration was not backing away from human rights concerns "because they fully support me speaking about human rights in the Security Council."

Egypt has long been one of Washington's closest allies in the Middle East, receiving $US1.3 billion ($1.71 billion) in US military aid annually.

Ahead of the visit, a US official said Mr Sisi would find a White House ready to soften US criticism of Egypt on human rights and to work on counter-terrorism, but unwilling to provide additional aid to the most populous Arab nation.

"He's going to get an end to finger-wagging [but] we're not giving him any more money," said the US official, who spoke on condition of anonymity.

"He's going to be disappointed because he wants more [financial] assistance and he's not going to get it."

It was not yet clear whether Egypt would escape a cut in its foreign aid as part of the Trump administration's plan to cut the overall State Department budget by 28.7 per cent.

ABC/wires