Thunberg has traveled halfway to the South American nation but will need to turn back to make the UN climate summit.
The activist refuses to fly due to high levels of emissions from air travel and instead uses boats, trains and electric cars to get around.
“It turns out I’ve traveled half around the world, the wrong way,” Thunberg wrote on Twitter. “Now I need to find a way to cross the Atlantic in November… If anyone could help me find transport I would be so grateful.”
Chilean President Sebastian Pinera said Wednesday that he was “deeply sorry for the problems and inconveniences” his decision would cause.
In the televised statement, he said that “as the president of all Chileans, I always have to put the problems and interests of Chileans first, their needs and hopes.”
Pinera also canceled the Asia-Pacific Economic Cooperation (APEC) Summit scheduled for November.
Chile’s protests began over a now-suspended price hike for subway tickets in Santiago. They expanded, revealing anger among ordinary Chileans who feel excluded from the nation’s economic rise. Many of the protesters are now asking for Pinera’s resignation.
The move also affects a group of 36 young climate activists crossing the Atlantic by sailboat to attend.
They were shocked to learn the event was canceled four weeks into their grueling voyage, after they set off from Amsterdam on October 2. They were using a sailboat highlight the impact of flying on greenhouse gas emissions.
The Sail to the COP group said in a statement Thursday that it had decided to sail on to Belém, Brazil.
“After the initial shock and sadness the news brought, everyone came together determined to continue what we started: putting the climate impact of aviation on the international agenda,” read a statement from the group.
Thunberg undertook her own 15-day trans-Atlantic voyage to New York in August in the high-tech, zero-emissions sailboat Malizia II to attend the UN Climate Action Summit in September.
CNN’s Jack Guy contributed reporting.