In a written statement, Altun said freelance journalist Johanna Cornelia Boersma's deportation was "not related to her journalistic activities."
"Turkish authorities have recently received intelligence from the Dutch police that Ms. Boersma had links to a designated terrorist organization and a request for information about her movements in and out of Turkey," the statement said.
Boersma works for Dutch daily Het Financieele Dagblad.
"A number of terrorist groups, including the PKK and Daesh, have carried out deadly attacks against Turkish citizens in recent years, killing more than 2,000 innocent people," Altun's statement said.
Altun said Turkey works closely with its allies, including the Netherlands, and relies on their insights to identify and neutralize threats against Turkish and European security.
To date, he added, "Turkish authorities, with help from their international partners, have blacklisted tens of thousands of individuals with links to terrorist organizations as part of an ongoing effort to combat extremism."