Images posted by social media users showed police and onlookers attending to numerous bodies lying amid pools of blood on the mosque floors.
Saudi Arabia’s civil defence authority provided a series of rising casualty numbers on its official Twitter account as ambulances whisked the wounded to hospitals. It said those injured in the disaster numbered 201.
A photo released by the authority showed police and workers in hard hats inspecting a pile of collapsed concrete slabs inside a part of the sprawling, ornately decorated mosque. Another showed the base of the toppled red-and-white crane tilted upward at a sharp angle.
Images aired on Saudi state television showed the crane’s metal boom smashed through what appeared to be the roof of the mosque.
Ahmed bin Mohammed al-Mansouri, the spokesman for the presidency of the Mecca and Medina mosque affairs, said that the accident happened during a severe storm carrying strong winds and heavy rain.
Authorities did not provide details on the victims’ nationalities, but it was likely that the tragedy will touch several countries.
The Grand Mosque and the cube-shaped Kaaba within it draw Muslims of all types from around the world throughout the year, though numbers increase significantly in the run-up to the hajj. The mosque is Islam’s holiest site to which Muslims face in daily prayers and a central site among the hajj rituals.
Performing the pilgrimage once during one’s lifetime is a duty for all able-bodied adult Muslims. This year’s pilgrimage is expected to start around September 22.
Mr Al-Mansouri said the crane, which was being used in construction work at the mosque, struck a circular area around the Kaaba and a nearby walkway.
The governor of the Mecca region, Prince Khalid al-Faisal, quickly called for the formation of a committee to investigate the cause of the accident.
Several cranes surround the mosque to support an ongoing expansion and other construction work that has transformed the area around the sanctuary.
Steep hills and low-rise traditional buildings that once surrounded the mosque have in recent years given way to shopping malls and luxury hotels - among them the world’s third-tallest building, a giant clock tower that is the centrepiece of the Abraj al-Bait complex.
The construction giant Saudi Binladin Group is leading the mosque expansion and also built the Abraj al-Bait project.
The Binladin family has been close to the ruling Al Saud family for decades and oversees major building projects around the country. The Binladen family disowned one of its many members, late al Qaida leader Osama bin Laden, in the 1990s.
It was not immediately clear who owned the crane that collapsed.
During the week of the hajj, Muslims converge on Mecca to perform a series of rituals, including the circling of the cube-shaped Kaaba, praying and holding vigil at Mount Arafat and perform the symbolic stoning of the devil by throwing pebbles at the three pillars in Mina.