The winner of eight Olympic sprinting titles, who retired from athletics in 2017, is currently on trial at Australia’s Central Coast Mariners.
Bolt, 32, scored two goals in a recent pre-season friendly but has not been offered a contract.
“Usain does not wish to pursue this Malta opportunity,” said his agent.
“There is a lot of interest in Usain playing football,” Ricky Simms also told ESPN. “We regularly receive similar approaches.”
In response, Valletta chief executive Ghasston Slimen said: “We wish Usain Bolt all the best with his football career. The Valletta FC offer is always on the table.”