The Trump administration has issued a rare rebuke of Saudi Arabia over the detention of two of the adult children of a former Saudi intelligence official who has been credited with protecting Americans from al-Qaida threats. A letter signed by a state department official said any persecution of Saad Aljabri’s family members by Saudi authorities was “unacceptable” and urged the “immediate release” of the two children, Omar and Sarah Aljabri, who were arrested from their home in Riyadh in March and have been held in detention indefinitely. The letter was released shortly after Aljabri filed a lawsuit against Mohammed bin Salman and other Saudi officials in a district court in Washington DC alleging that the Saudi crown prince was conspiring to kidnap and murder Aljabri from his home in Canada, where he has lived in exile. While details were scarce and could not be independently confirmed, the suit has alleged that Canadian authorities thwarted a plan by a Saudi hit squad to enter Canada and harm Aljabri just two weeks after the murder of the Washington Post journalist Jamal Khashoggi in a Saudi consulate in Istanbul. The state department letter, which was sent to the Democratic senator Patrick Leahy in response to his letter of concern about the safety of Aljabri’s children, also said the department had “repeatedly” requested the Saudi government clarify the status and nature of the children’s detention. “The strength of the US-Saudi partnership – which has benefited both nations for more than seven decades – permits us to engage in frank discussions in areas where we disagree,” wrote Ryan Kaldahl, acting assistant secretary for the bureau of legislative affairs at the state department. “The Department, in coordination with the White House and interagency colleagues, will continue to engage Saudi counterparts to resolve this situation in a manner that honours Dr Aljabri’s service to our country.” The letter is significant because the Trump administration has been reluctant to criticise human rights violations by the Saudi government even after the murder of Khashoggi, a US-based Saudi journalist. It is also noteworthy because the letter included high praise for Aljabri, who served as the US embassy in Riyadh’s counterpart on counter-terrorism. Aljabri, the letter said, had “responded around the clock to threats against our mission and personnel” and had kept US citizens safe. Saudi media outlets – and the Wall Street Journal, which called Aljabri a “fugitive” – have reported that the Saudi government has launched an investigation into Aljabri for corruption. But in its letter, the state department said any accusations of wrongdoing against Aljabri should be addressed through “established legal channels with full transparency and respect for the rule of law”. In what appeared to be an extraordinary defence of Aljabri, the letter added: “Should US interests be involved, the Department and interagency partners have open lines of communication with Saudi authorities to clarify and share information.” The Saudi embassy in Washington has declined to comment.