Sections of the Greece fans held up banners which referred to the massacre which had the words "knife, wire, Srebrenica" written on them.
"The Greek Football Federation deeply regrets the unacceptable banners containing fascist content during yesterday’s match between Greece and Bosnia-Herzegovina, which we condemn in the most absolute and unequivocal manner. These actions by a minority of supporters do not express in any way the views of the vast majority of Greek fans," read a statement from the Greek Football Federation.
"The Greek Football Federation feels obliged to apologise on behalf of the minority involved to the Football Federation of Bosnia-Herzegovina and the friendly people of that country".
The match ended 1-1 with Greece scoring a stoppage time equaliser.