"We are in mourning and offer deep condolences to the bereaved family members of the victims, including some prospective hajj pilgrims from Indonesia," President Jokowi said in a written statement made available to ANTARA in Jakarta on Saturday.
President Jokowi received information about the accident when he arrived in Jeddah on Friday night.
Cabinet Secretary Pramono Anung said the Indonesian Government has yet to confirm the number of Indonesian victims of the crane accident in Mecca.
"The number of victims is still confusing, but it is obvious that there are some from Indonesia," Anung said.
But The Wall Street Journal reported on its website that the crane accident killed at least 107 people.
Quoting Saudi officials, the Journal said the deadly accident occurred days before the start of the annual Hajj pilgrimage that will see more than two million religious tourists visit the holy city of Mecca.
Government officials said a storm that rocked the city on Friday caused the cranes collapse, which caved in parts of the mosque, the worlds largest, which was filled with pilgrims when the crane collapsed.
Footage aired by state television showed police and medical teams attending to bloodied bodies on the mosques white marble floors, as high winds and heavy rains lashed the site.
An additional 238 people were reported injured, according to the official Twitter account of the nations Civil Defense department.
Also, a spokesman for the health department in Mecca region said it was still working to identify the nationalities of the victims.
Prince Khaled al-Faisal, the governor of Mecca, ordered an immediate investigation into the accident, Saudi state television said. He later visited the accident site and instructed officials to begin repairs as soon as possible.
The Grand Mosque attracts Muslims from throughout the world for the Hajj. Millions, dressed in simple white clothing, perform prayer rituals for what is often a once-in-a-lifetime religious pilgrimage.
Yet the massive crowds have contributed to several tragedies at Islams holiest of sites, mostly due to stampedes.
The last deadly incident occurred in 2006, when 346 pilgrims were killed in a stampede on Mecca bridge. In 1990, a stampede in a pedestrian tunnel in the city killed 1,426 pilgrims, the deadliest Hajj incident in recent history.(*)