Rebecca Gomperts, the doctor who in 1999 founded the Women on Waves Foundation which manages the clinic, said on Saturday the ship would stay in international waters until it found a way to carry out its intended mission.
"The ship is not going to leave, it is going to stay there," she told a televised news conference in the central Portuguese city of Coimbra.
"We are here with the intention to help Portuguese women and we will do all we can to do that," she added.
The ship requested permission late on Friday to dock in the northern port of Figueira da Foz where it planned to stay for two weeks to hand out abortion pills to women with unwanted pregnancies of up to six-and-a-half weeks.
But Portugal's centre-right government earlier on Saturday refused to give the vessel permission to enter national waters arguing the measure was intended to ensure the staunchly Roman Catholic country's laws against abortion were respected.
"It is a question of legality and not of morality," Secretary of State for Sea Affairs, Nuno Fernandes Thomaz, told national news agency Lusa.
"If we accept that third parties come and violate our laws it would become much more difficult to impose authority amongst the Portuguese."
It is the first time that the ship, which visited Ireland in 2001 and Poland two years later, has been refused entry into a country.
The vessel is currently off the coast of northern Spain, not far from the Portuguese border.
Abortion is banned in Portugal except when the mother's life is in danger, or in certain specified conditions such as the risk of damage to physical or mental health, sexual violence or possible congenital deformity.
"It is a question of legality and not of morality"
Nuno Fernandes Thomaz,
Secretary of State for Sea Affairs
Family planning agencies estimate between 20,000 and 40,000 illegal abortions, some of them fatal, are carried out in Portugal each year.
Thousands more women go abroad each year to terminate their unwanted pregnancies.
Polls show a majority of Portuguese favour a loosening of the nation's abortion laws, which are among the most conservative in Europe.
But in March Portugal's centre-right government used its slim majority in parliament to vote down proposals by left-wing parties which would have eased access to abortion.
The Social Democratic Party has given its junior coalition partner, the right-wing Popular Party, assurances that it would not modify the law nor call a referendum on the question before the end of its mandate in 2006.