The Haj pilgrimage, which starts next week, will proceed unaffected by the incident, Saudi officials confirmed.
Director General Suleiman bin Abdullah Al Amro told satellite broadcaster Al Arabiya on Saturday that unusually powerful winds in the area also tore down trees and signs as a storm whipped through the area.
As world leaders offered condolences, the governor of Makkah region, Prince Khaled Al Faisal, ordered an investigation into the incident.
This comes as the first official response to suggestions that Gulf states should do more to address the plight of Syrian refugees.
At least 107 people died when the crane toppled into a courtyard of the mosque during extremely high winds on Friday.
At least 107 people were killed and 238 injured after a crane collapsed on to the Grand Mosque in Saudi Arabia's holy city of Makkah.
The civil defence agency said on Twitter that emergency teams were sent to the scene after a crane fell at the holy city of Makkah's Grand Mosque.
Risk services company says says this year's Haj is likely to be among the hottest in the past two decades.
184 injured as storm causes huge crane to crash into Grand Mosque.
So far, the group's presence in the kingdom appears to be in a low-level stage, but it has claimed four significant bombings since May, one of them in neighbouring Kuwait.