The Moroccan government blocked the harbor with warships, with the Health Ministry saying Wednesday it did not authorize the ship's visit or any procedures by non-resident physicians, CNN reported Thursday.
Abortion is illegal in Morocco.
The abortion ship is run by Women on Waves, founded in 1999 by a Dutch doctor to provide abortions to women in countries where it is illegal.
A Women on Waves member told CNN she and others were demonstrating in front of the marina in Smir and that police were present.
She said police told her she was "not authorized" to be there.
"I am not going to be intimidated by them," she told CNN before the phone conversation cut out.
The ship takes women into international waters to perform the abortions, which are legal under Dutch law until 6 1/2 weeks into the pregnancy, CNN said.
Gunilla Kleiverda, a gynecologist aboard the vessel, told CNN she would not be "practicing as a gynecologist in Morocco."
"We are not going to perform any abortions within Morocco," she said. "We are sailing out with women to international waters where ... the Dutch law applies."
The group also wants to tell Moroccan women that an abortion-inducement drug is available to them, the BBC said. However, most of the women were unaware of its availability.
The ship has been to Ireland, Poland, Portugal and Spain, the organization said, but this week's trip to Morocco is its first attempt to offer abortions in an Islamic country.