President Barack Obama Thursday raised the fate of jailed journalists in Egypt and his concerns over political repression in his first meeting with President Abdel Fattah El-Sisi, US officials said.

Obama and Sisi met on the sidelines of the UN General Assembly in New York, as Washington and Cairo gingerly seek common ground after a period of turmoil that followed the toppling by Sisi, a former army chief, of Egypt's Islamist Mohamed Morsi last year.

Deputy National Security advisor Ben Rhodes told reporters aboard Air Force One that the talks were "productive" and focused on issues wracking the Middle East, including US operations to take on the Islamic State group and counter-terrorism.

Rhodes said that Obama specifically raised "our ongoing concerns about Egypt's political trajectory. They had a frank exchange on those issues," Rhodes said.

"The president raised a number of specific concerns that we have related to human rights," Rhodes said, including the rights to free speech and the rights of journalists.

"The president expressed his view that those journalists should be released."

Washington has frequently raised the plight of three Al-Jazeera journalists jailed by Egypt after being accused of ties with Islamists.

Australian Peter Greste, Egyptian-Canadian Mohamed Fadel Fahmy and Egyptian producer Baher Mohamed were convicted in June of aiding the blacklisted Muslim Brotherhood and spreading false news that portrayed Egypt as being in a state of "civil war".

Greste and Fahmy received seven-year terms, while Mohamed was sentenced to 10 years, in a case that sparked international outrage.

Eleven defendants tried in absentia, including one Dutch and two British journalists, were given 10-year sentences.