The IMF said in a statement on late Tuesday that Lagarde's trip to the Middle East was "postponed" for the conference.
It's an abrupt change of position from the manager of the fund, who said only on Saturday that she was still planning to attend the event, though he did was frightened by reports of Khashoggi's disappearance.
The Saudi journalist who contributed to the Washington Post has not been seen since joining the Saudi consulate in Istanbul on October 2.
Lagarde said on Saturday that her job was "to guide the affairs of the IMF in every corner of the world and with many governments." But she added that in the next few days "they would be very attentive to the information that will come out ".
The IMF did not respond late Tuesday to a request for further comments on its plans change.  US Treasury Secretary Steven Mnuchin is among the high-ranking figures who say they still intend to attend the Saudi conference, part of Crown Prince Mohammed bin Salman's plan to reshape the country's oil-dependent economy.