Detective Inspector Greg Huchins said it would be alleged the offences occurred at the Meningie property where the man was taken into custody.
"That person is currently in the Murray Bridge Police Station where we will be refusing bail," he told reporters on Saturday.
The man is expected to appear in the Murray Bridge Magistrates Court on Monday.
The backpacker is still being cared for by police as she continues to recover.
"She is still with police, she is well, unharmed and obviously her family is very grateful that she is safe," Insp Huchins said.
The backpacker had left her tourist accommodation in Adelaide's CBD and boarded a bus to Murray Bridge on Thursday morning.
From there it was thought she had been picked up by someone in a red ute.
Late on Friday police received information from a member of the public which led them to a house at Murray Bridge where they found the woman. The backpacker arrived in Adelaide on February 2 and visited Kangaroo Island before returning to the city on February 6.
Facebook posts revealed she had also visited Sydney and Tasmania on her travels in what was planned to be an extended period in Australia.
It is unclear if she will return to Belgium or stay on in Australia.
- AAP