He then offered Sweeney $5,000 to take the account down and help stop "crazy people" from following his flights.
"I don't love the idea of being shot by a nutcase," Musk wrote.
The college freshman has developed more than 12 other flight bot accounts that track the flights of tech celebrities like Jeff Bezos and Bill Gates.
Sweeney countered with a request for $50,000, adding that he could use the money to pay for college and maybe buy a Tesla Model 3.
On January 19, Musk sent a final message that said it didn't feel right "to pay to shut this down".
In response, Sweeney wrote, "options other than remuneration like an internship would make taking it down a lot easier."
However, the SpaceX fan did give Musk some advice and recommended a blocking program that would prevent flight tracing.
Musk reportedly took the advice, making it harder but not impossible for Sweeney to still track and tweet his movements.
"It's just a bit more complicated," the young man said.
On his website, linked into his Twitter bio, Sweeney encourages people to "please consider donating" as he spends "a good amount of time running, keeping up and developing new features for these Twitter accounts."
Elon Musk has previously voiced concerns about his travel details being made public.
In January he said accounts dedicated to sharing information about his movements were "become a security issue."
