The council's planning department have said the Dublin Port Company's scheme to reclaim 52 acres from the bay would be against the city's development plan.
Some councillors repeated the report's conclusion that the planning application to An Bord Pleanála is premature pending a number of studies on the future of Dublin Bay.
Cllr Gerry Breen (FG) said the port company had been crying wolf for 36 years saying they were operating at near capacity.
And he pointed out that the Environmental Protection Agency had advised against any infill in the bay because it may exacerbate flooding.
Cllr Bronwen Maher (Green Party) said the port's plan was illogical given current on-going studies and the fact that much of the proposed infill is in area protected by conservation laws.
But Cllr Bill Tormey (FG) said the proposed alternative site for a port at Bremore near Balbriggan was in never never land and he supported the extension, saying that a fortune had been spent on the Port Tunnel.
But the monthly city council meeting agreed that the objection should go forward.
Three councillors who are directors of Dublin Port objected to having to absent themselves during the debate following legal advice that there could be a conflict of interest.
