SL is also demanding an apology for the "offence caused to the affected passengers."
"We will forward our demand to Konstfack's management on Sunday. To us this is completely unacceptable," SL's Christer G Wennerholm said to the Dagens Nyheter newspaper.
Swedish culture minister Lena Adelsohn Liljeroth expressed anger on Saturday after seeing the film of the art student's work.
"I do not think that vandalism is art. And I presume that Konstfack does not intend to pay for the train car," she said at the Market art fair in Stockholm.
The minister's reaction came after watching the two minute long film, "Territorial pissing" which features a masked graffiti artist splashing masses of paint in front of a crowd of metro passengers. The artist also then breaks a window.