"However, we have heard a funeral will take place in the coming two or three days", he said before adding that it was unknown if Khashoggi's body will be present at the funeral.
But other Turkish officials have said they believe that Khashoggi was killed by Saudi agents inside the consulate.
Erdogan's comments were his most direct suggestion yet of potential Saudi culpability in Khashoggi's disappearance. He also said he believes Turkish officials soon will announce the findings of their investigation.
Turkish President Recep Tayyip Erdogan asked the Saudi government on Monday to prove that Khashoggi had left the consulate building in Istanbul while Washington urged Riyadh to support an investigation into his disappearance.
He said the consulate was equipped with cameras but they did not record footage, so no images could be retrieved of Khashoggi entering or leaving the consulate, which is ringed by police barriers and has high security fences topped with barbed wire.
The reporter, who was a former government advisor, was self-exiled in the USA in 2017 as he was afraid of a possible arrest, following his criticism on the decisions of Saudi Prince, Mohamed Ben Salman, and Riyadh's military intervention in Yemen.
The Turkish government is looking into Khashoggi's disappearance.
U.S. officials have stated that they are following this case closely.
Mohammad al-Otaibi, the Saudi consul-general in Istanbul, opened the mission up to Reuters Saturday to show the missing journalist was not on the premises.
Trump, whose first overseas trip as USA president was to the kingdom and whose son-in-law Jared Kushner has close ties to Prince Mohammed, said Tuesday he had not yet talked to the Saudis about Khashoggi, "but I will be at some point".
"If the worst-case scenario is realized, Saudi Arabia will have links to the murder of a vocal critic in a fashion engineered to create just enough doubt for the veneer of implausible-but-sufficient deniability", the New York-based Soufan Center said Tuesday.
Khashoggi's fiance Hatice Cengiz believes that Khashoggi was not killed.
That harshness corresponds with the growing concerns internationally about the direction Saudi Arabia is taking under Prince Mohammed and his father. He has written multiple columns recently in The Washington Post where he criticized Crown Prince Mohammed bin Salman. "There's no difference between the state terror and other terror actions", she added.
The relationship between Saudi Arabia and Turkey has always been contentious.
In his writings for the Washington Post, the Saudi commentator had slammed the Saudi regime policies towards Qatar and Canada, the war in Yemen, and a crackdown on dissent and the media in the kingdom.
Khashoggi, a former Saudi government adviser, had been living in self-imposed exile in the United States since previous year fearing possible arrest. Police also said a special team of around 15 Saudis were especially sent to Istanbul and in the building at the same time as Khashoggi.
Trump said he didn't know what happened to Jamal Khashoggi and expressed hope that the 59-year-old writer, who went missing a week ago, was still alive.