Mike Pompeo, the US secretary of state, has privately urged Crown Prince Mohammed bin Salman, the heir to the Saudi throne, to cut his ties to a close adviser whom the US has sanctioned for his alleged role in the murder of journalist Jamal Khashoggi.

Pompeo is understood to have raised his concerns about Saud al-Qahtani in private conversations with Prince Mohammed and his brother Khalid bin Salman.

US authorities believe that Qahtani, a former aide to the crown prince, oversaw the team that killed Khashoggi in the Saudi consulate in Istanbul. He is thought to have remained a confidant of Prince Mohammed despite having a lower profile in recent months.

The advice to sideline Qahtani comes at a time when Pompeo’s support for Saudi Arabia is facing intense scrutiny in Congress, where the Trump administration has been criticised for not condemning Saudi Arabia strongly enough following Khashoggi’s murder last year.

A state department spokesperson told the Guardian it would not discuss details of private diplomatic conversations.

Qahtani was publicly rebuked after the Khashoggi murder, when Saudi’s ruler, King Salman, had his son’s adviser removed from his role at the royal court.

The decision was seen as an acknowledgment that the powerful aide and social media tsar had a role in the plot to murder Khashoggi.

But within months reports emerged that Qahtani was still communicating with the young crown prince – who is known as MBS – and was actively participating in his crackdown against dissidents.

Some reports, and one human rights activist who spoke to the Guardian, also linked Qahtani to allegations of torture against female political prisoners.

The Guardian has been told that Qahtani, who formerly served as the head of Saudi’s cyber-unit, is still actively engaged in a similar role within Prince Mohammed’s private office.

According to a source with knowledge of the matter, the crown prince has remained loyal to Qahtani. “I am not sure MBS will take any notice of the US over this,” the source said.

A spokesman for the Saudi embassy in Washington did not respond to requests for comment about Qahtani’s role in the kingdom or the claims made against him by the US government.

Qahtani is now on two official sanctions lists.

Jamal Khashoggi, pictured in December 2014. Photograph: Mohammed al-Shaikh/AFP/Getty Images

Last November the US Treasury said Qahtani was “part of the planning and execution of the operation that led to the killing of Mr Khashoggi”.

The Treasury said Qahtani was one of the Saudi officials involved in “the abhorrent killing” of the journalist in a targeted and brutal operation.

Earlier this week the state department included Qahtani on a list of 16 individuals who have been barred from entering the US because of their alleged role in the killing.

The notice was issued, the state department said, because it “has credible information that officials of foreign governments have been involved in significant corruption or gross violations of human rights”.

The Saudi government has said the Khashoggi murder was a rogue operation and has denied the crown prince had any role in it.

The Saudi minister of state for foreign affairs, Adel al-Jubeir, said: “The crown prince was not aware of this … This was an operation where individuals ended up exceeding the authorities and responsibilities they had. They made a mistake when they killed Jamal Khashoggi in the consulate, and they tried to cover up for it.”

But the CIA is widely reported to have concluded with a medium-to-high degree of confidence that the crown prince ordered the murder .

Bruce Riedel, a director of the Brookings Intelligence Project and 30-year veteran of the CIA, said Pompeo’s private effort to force Mohammed to cut ties to Qahtani proved that the “cover story” concocted by the Saudis was “not working”.

“No one is taking it seriously, so this is a sign of increasing desperation, and that now they are going to try to throw [bin Salman’s] top henchman under the bus and blame it on him, and he will be the ‘rogue operator’,” Riedel said.

He added: “I don’t think that will pass muster either because there is all kinds of evidence that Qahtani works closely with MBS on this operation and other operations.”

The crown prince was considered “persona non grata” in most democratic parts of the world, Riedel said, apart from the White House. Hopes within the Trump administration that the Khashoggi murder would “fade away” have not materialised, he added.

Pompeo’s condemnation of Qahtani comes at a turbulent time for Saudi in Washington. While the crown prince has received steadfast support from his closest allies – Trump, the president’s son-in-law Jared Kushner, and Pompeo – the country is coming under fire on Capitol Hill, which earlier this month voted to end American military assistance for Saudi’s war in Yemen.

There is also increasing speculation about the whereabouts of the kingdom’s incoming ambassador to the US, Princess Reema bint Bandar Al Saud, who was named to her new role by MBS in February. Bandar has not yet been sworn in as a diplomat or as a minister by King Salman and has been largely absent from the press except for appointment to serve as the head of the Saudi Special Olympics Federation, which was announced in March.