Advani, who led the BJP in the 2009 Lok Sabha battle which it lost, kept away from the Goa national executive meet citing poor health.
"For some time I have been finding it difficult to reconcile either with the current functioning of the party, or the direction in which it is going," said Advani, increasingly overshadowed in the BJP by second rung leaders.
He said he no longer had "the feeling that this is the same idealistic party" formed in 1951 by Shyama Prasad Mookerji, Pandit Deen Dayal Upadhyay, Nanaji Deshmukh and Atal Bihari Vajpayee "whose sole concern was the country and its people".
"Most leaders of ours are now concerned just with their personal agendas," said Advani, in one of the harshest condemnation of BJP leaders by anyone within, bringing its internal rift out in the open.
"I have decided, therefore, to resign from the three main fora of the party: national executive, parliamentary board and the election committee. This may be regarded as my resignation letter."