The action by Spain is the latest instance of a government moving to deport Taiwanese to the self-governing island's rival.
Beijing views Taiwan as its own territory without sovereign legal status.
The Taiwanese ministry said in a statement Sunday that it "deeply regrets" a decision by the Spanish government to agree to a request by Beijing to extradite 269 Taiwanese and Chinese nationals arrested in December in Spain.
Taiwanese media reports said more than 200 of the suspects are Taiwanese.
Chinese authorities say they should try the cases because their citizens have been swindled out of millions of dollars.