A State Department official declined to say whether the two discussed Khashoggi's status, citing "private diplomatic discussions".
Turkish and Saudi authorities gave conflicting accounts on Wednesday about the whereabouts of Saudi commentator Jamal Khashoggi, who moved to Washington past year fearing retribution for his views and has not been seen almost 30 hours after entering the Saudi consulate in Istanbul.
"The consulate confirmed that it was carrying out follow-up procedures in coordination with the Turkish local authorities to uncover the circumstances of the disappearance of Jamal Khashoggi after departing the Consulate", it added.
A spokesman for Turkish President Recep Tayyip Erdogan told reporters on Wednesday night that authorities believed the journalist was still there.
"According to the information we have, this person who is a Saudi citizen is still at the Saudi consulate in Istanbul", Ibrahim Kalin said. "We are monitoring the situation closely, trying to gather more information".
Hatice said she waited for Khashoggi outside the consulate from about 13:00 (10:00 GMT) until after midnight and did not see him leave.
She said Khashoggi had left his mobile phone with her.
"After 9 pm, more than five hours after the consulate had closed, his friend and fiancée were still waiting outside the consulate in the dark for Khashoggi to come out", Hatice said. "I can't even guess how such a thing can happen to him", she told The Associated Press.
He went into a self-imposed exile in the United States following the ascension of Prince Mohammed, now next in line to the throne to his father, the 82-year-old King Salman.
After several of his friends were arrested, his column was cancelled by the Al-Hayat newspaper and he was allegedly warned to stop tweeting, Khashoggi left Saudi Arabia for the USA, from where he wrote opinion pieces for the Washington Post and continued to appear on Arab and Western TV channels.
Jamal Khashoggi, a contributor to the Washington Post, went to the Saudi consulate on Tuesday to receive an official document for his marriage and has not appeared since. "I hope it will be resolved peacefully", he said.
Turkey has summoned Saudi Arabia's ambassador in Ankara on Thursday over the disappearance of a Saudi journalist.
Khashoggi maintained ties with Saudi elites and launched a satellite news channel, Al-Arab, from Bahrain in 2015 with the backing of Saudi billionaire Prince Alwaleed bin Talal.
As a journalist, he interviewed al-Qaeda leader Osama bin Laden several times in Afghanistan and Sudan, and served twice as editor of Al Watan newspaper.
Scores of businessmen were detained last November in Riyadh's Ritz-Carlton hotel in a separate campaign against corruption, unnerving some foreign investors.
Press freedom groups have decried Khashoggi's disappearance.
Ali Shihabi, head of the Arabia Foundation in Washington which regularly supports Saudi policy, expressed concern on Twitter about the reports.
He failed to emerge from the building, with his fiancé raising the alarm and Turkish authorities investigating the incident.