Over 50 fishermen had taken action when the Faroese fishing trawler The Jupiter arrived at the port on Tuesday, and it was forced to leave.
It came amid concerns about mackerel quotas in the Faroe Islands.
The Jupiter has now returned to its home port, and skipper Emil Pedersen said its catch would now have to go into meal or oil production.
The Faroese has declared a quota of 85,000 tonnes for this year. Previously, Iceland awarded itself 130,000 tonnes.
Scotland’s First Minister Alex Salmond has called for political action to end the ongoing mackerel dispute, which it has been claimed could have serious consequences for the Scottish fishing fleet.
Mackerel is the most valuable stock to the Scottish industry
Meanwhile, Ian Gatt, the leader of Scotland’s pelagic fishing industry, said the protest at Peterhead sent a “Strong Message” to the two countries that their mackerel was not welcome on Scottish shores.
Mr Gatt said the crews did not take glory from the protest. He said: “This was not about getting a victory, it was about sending a message to the Faroe Islands and Iceland that the mackerel they catch will not be welcome in Scotland”.
