By a vote of five to two, the appeals judges overturned the Mecca criminal court's decision that it had no jurisdiction over allegations of "safety breaches", the Okaz and Saudi Gazette newspapers reported.
At least 109 people, including foreign pilgrims, were killed when the crane crashed into a courtyard of Mecca's Grand Mosque during high winds in September 2015.
The mosque draws millions of pilgrims from around the world each year.
The accused included at least one Saudi "billionaire" and nationals of Pakistan, the Philippines, Canada and several Arab countries, the newspapers reported.
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They gave no details of when hearings might resume, and have given differing figures for the number of accused, which are either 13 or 14.
The accused were charged with "negligence leading to death, damaging public property and ignoring safety guidelines", Okaz and Saudi Gazette said.
The crane was one of several the Saudi Binladin Group had erected as part of a multi-billion-dollar expansion plan to accommodate increasing numbers of faithful.
Saudi Binladin Group, which developed landmark buildings in the kingdom, was founded more than 80 years ago by the father of Al-Qaeda leader Osama bin Laden, who was killed by US commandos in Pakistan in 2011.