Former Chinese President Hu Jintao is also under investigation although his arrest has not been sought. When he was named in the probe, China's Foreign Ministry said the Tibetan issue was a Chinese matter, adding that it hoped Spain would handle this issue properly.
Spain's legal system recognizes the universal justice principle, under which genocide suspects can be put on trial outside their home country.
The policy allowed former judge Baltasar Garzon to try to chase late al-Qaida leader Osama bin Laden and late Chilean dictator Augusto Pinochet.
In practice, very few probes have seen people brought to trial in Spain. Meanwhile, the investigations have irked some countries, most notably China and Israel, and led to accusations that Spain was behaving like a global policeman.
Alan Cantos, president of Spain's Tibet Support Committee, which first pressed for the probe in 2008, expressed satisfaction with the court decision but was not overly optimistic that anyone would be brought to trial.
The court must process the arrest orders via Interpol.
"It's not easy, but it's a big step," Cantos told The Associated Press. "They are stuck in their own country and a competent court is pointing the finger at them. It's so they don't have it too easy."
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Alan Clendenning contributed to this report.