The 269 Chinese and Taiwanese telecom scam suspects were caught in Spain in December, according to Taiwan's foreign affairs ministry.
More than 200 in the group are from the island.
The ministry said Spanish authorities decided Friday to send the group to the mainland at China's request, against the suspects' will.
"This decision has infringed upon our people's rights and interests, as well as ignoring the EU's tradition of placing high value on human rights," according to a statement from the ministry.
Taiwan had demanded the suspects be deported back to the island, but Spain had not responded, it said.
Relations have worsened with China after Taiwan's President Tsai Ing-wen came to power last May because she has refused to recognise the island is part of "one China."
The deportation cases are seen as a bid to pile pressure on Tsai by Beijing, which sees Taiwan as a breakaway province to be brought back within its fold.
Since then, China has insisted that Taiwanese scammers caught abroad are deported to the mainland to face trial, including from countries including Armenia, Cambodia and Kenya.
Taiwan last November passed a bill to crack down on swindlers committing crimes overseas.
Since 2011, nearly 2,000 Taiwanese fraud suspects have been arrested abroad, according to Taiwan's Criminal Investigation Bureau.