The former Arsenal and Middlesbrough striker scored 15 goals last season, helping Les Merlus finish eighth in Ligue 1.
Gourcuff admitted that he is "annoyed" by the Aliadiere's stance but added that he will not stand in his way if he wants to leave.
"Jeremie is not happy and I am annoyed with that," the 58-year-old told L'Equipe. "But there is no problem, it is just that Jeremie is discontent. I won't veto anything.
"When a player is not at ease in a club there is little chance he would give his best. But there has been no proposition, so it is a bit complex."
Lorient are said to value Aliadiere, who has two years remaining on his contract, at around €8m (£6.9m).