Around a hundred protesters earlier occupied part of the airport reserved for private jet parking, after breaking down a gate, the Royal Marechaussee (border police) said in a tweet.
"Protesters have been asked since 2 pm (1300 GMT) to voluntarily leave the terrain. The Marechaussee and police are now making arrests," police said.
Dutch media reports said the Extinction Rebellion protesters gathered on a lawn between hangars but were prevented by officers from getting access to the apron.
Many carried banners and posters and accused Eindhoven airport -- which handles international flights -- from causing air and noise pollution damaging to public health.
Some scheduled flights were scrapped on Friday as a precaution ahead of the planned protest, but flight operations on Saturday were not affected, an airport representative told the ANP news agency.
Meanwhile Eindhoven airport in a statement said it shared the activists' view "that aviation, like other sectors, needs to (quickly) become more sustainable."
"We also feel that sense of urgency. It is partly for this reason that we are not pursuing growth for our air traffic, and instead are prioritising the sustainability of existing air traffic," the airport said on its website.
Dutch police in November arrested hundreds of climate activists after they stormed an apron at Amsterdam's Schiphol airport.
The protesters then cycled around on the apron and sat in front of private aircraft to prevent them from leaving, before being escorted by police to waiting buses to be taken away.
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