Protesters flung red paint and eggs as a Dutch ship finally entered a Polish port on Sunday to offer abortion advice to the staunchly Roman Catholic country's women.
A Polish church leader said the ship wanted to "kill Poles"
The arrival of the Women on Waves ship, which had originally hoped to dock on Friday night, has caused a storm of controversy.
Anti-abortion campaigners say the ship is trying to import a banned abortion pill into Poland.
The port chief in Wladyslawowo, north of Gdansk, said the Langenort had not received permission to dock and could still be asked to leave.
"If someone does not respect our regulations, they have to be aware of the consequences," Kazimierz Undro told the Polish news agency PAP.
Women on Waves earlier complained that they were initially kept out of the port on the pretext of poor weather and said the port authorities had failed to provide a promised pilot to bring the ship in.
About 200 young protesters, said to be mainly Polish nationalists, pelted the Langenort with paint and eggs from a pier.
Women on Waves uses the ship to offer the abortion pill to pregnant women in countries where abortion is illegal.
It docks in international waters and members of Women on Waves offer advice and treatment to women who come on board.
The floating clinic, which is licensed by the Dutch Government, was invited to Poland by local women's rights groups.
On board are two doctors and a nurse who are able to provide counselling, contraceptives and the abortion pill to women no more than six and a half weeks pregnant.
To circumvent strict Polish anti-abortion laws, the group plans to take women aboard and sail 20 kilometres (12 miles) out into international waters to administer the pills.
'Hospital of death'
It is up against fierce opposition from Polish anti-abortion groups and nationalist political parties, who have dubbed the ship "the hospital of death".
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The Archbishop of Gdansk, Tadeusz Goclowski, has described the boat's mission as an attempt
to "kill Poles."
Abortion has been illegal in Poland since 1993.
It is only allowed in cases of rape or where the health of the mother or embryo is in danger.
Many Poles look to the Polish Pope, John Paul II, as the highest moral authority.