The vote was on a draft Commission regulation proposed in the wake of Iceland and the Faroe's failure to reach agreement with the EU and Norway on mackerel quotas.
It comes a month after the North Sea and Atlantic mackerel fisheries lost their Marine Stewardship Council accreditation as a result of the ongoing dispute.
Following the meeting, Commissioner Damanaki stated: "We expect from Iceland and the Faroe Islands to come back to the negotiating table in a responsible manner and to fully respect the sustainability of the mackerel stock."
"Today's debate in the European Parliament on the trade instrument against unsustainably fishing countries marks an important step in its adoption process. If there is no agreement soon, this trade instrument will be put into effect. I conveyed the message that the EU and Norway have to fully cooperate on this."
"Along with Norway, we are determined to seek those solutions that, in any case, will not put at risk the sustainability of the mackerel stock, for the benefit of fishermen and coastal communities."
Scottish National Party President Ian Hudghton MEP also welcomed the European Parliament's Fisheries Committee backing possible EU sanctions against countries embarking on non-sustainable fishing.
Mr Hudghton commented: "The European Parliament has sent out the strong message that a deal must be reached on the important mackerel fish stocks. These stocks have previously been fished sustainably and they are of huge economic significance.
"It is rare for the parliament's Fisheries Committee to vote unanimously given that its members represent a variety of interests. Nevertheless, today MEPs representing all groups - north and south, the industry and environmentalists - united to back possible sanctions.
"It is important for everyone, including the Icelandic and Faroese industries, that a solution is found. Hopefully the parliament's message will go some way in hastening a satisfactory conclusion."
EU Sanctions for Non-Sustainable Fishing gets Vote
EU - The European Parliament's Fisheries Committee has backed proposals for EU sanctions against countries that do not fish sustainably.
by Lucy Towers