"Indonesia supports Saudi Arabia's bid to host the FIFA World Cup in 2034," Thohir said in a statement.
"Indonesia continues to prepare for its bid to host the FIFA World Cup after 2034, as well as other FIFA competitions."
FIFA has invited bids from Asia and Oceania for the 2034 tournament, setting a deadline of October 31.
Thohir said last week he had held discussions with his Australian counterpart about a possible bid that could also have included Malaysia and Singapore.
Football Australia has previously said they were exploring the possibility of bidding for the tournament.