Bayern are keen to land the Spanish internationalist in a deal rumoured to be worth 20 million Euros.
"It does not look too good right now," said Hoeness. "The people at Bilbao are very, very stubborn and do everything they can to stop this transfer from happening."
Martinez and Fernando Llorente have been left out of Athletic's match against HJK Helsinki in the first leg of the Europa League on Thursday.
Bilbao are trying to replicate their run to the final of the Europa League last season when they lost 3-0 to La Liga rivals Atletico Madrid in the final.