Phillip Lacey is credited with bringing the livestock trade to the West Sussex port and in recent weeks has been at loggerheads with the port's board of trustees.
Shoreham has been the scene of a month of vociferous protests against the trade, in which more than 1,000 police were often needed to ensure lorries could enter. The police operation has so far cost about £3.5m and an extra £4.5m has already been budgeted for.
The board and the two local authorities which have an interest in the port have been searching for a way to end the livestock business at Shoreham.The board had promised to end the trade as soon as the existing contracts had expired but Mr Lacey last week angered protesters by insisting the trade would go on.
Mr Lacey, general manager of the port for 11 years, said: "As far as I'm concerned the law of the open ports applies whether or not there is a contract.
"I see no reason for the trade to be stopped, the degree of disruption has been unfortunate, but not enough to prejudice the rights of other users."
Preparations for a lengthy siege continued after the authority announced the decision to stop the trade, leading many protesters to question the sincerity of the board's decision. But the board reacted by progressively stripping Mr Lacey's powers.
Adur District Council yesterday blocked the trade from Sunday after discovering the harbour did not have the appropriate planning permission for the berth used by the haulage ship.
Pat Hawkes, a member of the board and also a Brighton Labour councillor, welcomed Mr Lacey's decision and said that his resignation would be accepted at the next board meeting on 27 February.
He added: "He will tender his resignation but unfortunately he has to give six months' notice so he won't be leaving before August - unless we can get rid of him sooner."
National groups campaigning against the trade also said that Mr Lacey could not leave too soon.
Mark Glover, of Respect for Animals, said: "Lacey is an accessory to a crime against our fellow creatures and has consigned countless animals to a life of hell. Good riddance."
Mr Lacey has also come under increasing pressure from his own staff. Last week a petition was presented to him, signed by all but two of his employees, urging him to halt the trade immediately.
Last week a spokesman for the staff said that they would do "all they could from inside the port to bring an end to the live animal trade".Reuse content