The fans were reported by the referee and the match commissioner to have thrown bottles of water lighters coins and flagpoles on to the pitch. They also lit a number of flares and stormed the pitch at the end of the match.
'The Albanian soccer federation has appealed against the decision at the FIFA appeal commission' Albania's soccer federation said in a statement on Thursday.
'This is an extremely harsh decision because the experience of international matches in Albania shows they have been free of violence and vandalism against visiting teams.'
However the federation reminded fans who are ethnic Albanians from Kosovo and Macedonia as well as Albania the 'bitter and isolated case' should serve as an 'alarm bell'.
It was the second time in five months Albania have been fined by FIFA following a 14000 Swiss franc sanction imposed last October for similar incidents.
'We want to remind the public ... that violence in stadiums all over the world could even be punished with the expulsion from international competitions' the statement added.
Albania's team has credited the enthusiastic support of their fans for their success at home including the defeat of European champions Greece in September.
Albania's European Group Two home qualifiers against Georgia on June 4 and Kazakhstan on September 3 will take place behind closed doors. Albania are fifth in the group with six points.