The Dutch non-profit group, Women on Waves, offers free abortion services to women in countries where the procedure is banned.
It takes women in the early stages of pregnancy out to international waters, where the abortion is performed.
Abortion is banned in the predominantly Roman Catholic nation, except to save the mother's life.
The Army said it had been instructed by President Jimmy Morales to act, and would defend "human life and the laws of our country" by preventing the group from carrying out abortions.
Officials are preventing activists from disembarking from the ship, and women will not be allowed to board the boat, reports say.
The Women on Waves' boat docked on the Pacific Ocean port of Quetzal, in the city of San Jose, on Wednesday.
The group says it has a legal permit to sail in Guatemalan waters and the boat is being illegally "detained" by the authorities.
It had planned to stay in the country for five days.
The group says more than 60,000 illegal abortions are performed in Guatemala every year, and most of the women who put their lives at risk at the hands of untrained professionals are poor.
"We respect religious beliefs but this [abortion] is a fundamental right in a democracy," spokeswoman Leticia Zevich told La Hora Newspaper.
However, Guatemala's Catholic Church, other religious leaders and politicians protested against the presence of the boat.
"The boat of death has arrived in Guatemala," said lawmaker Raul Romero during a Congress session earlier on Wednesday.
In most Latin American countries, abortion is either illegal or only allowed to save the life of the woman.
The Guatemalan army says it will block the activities of a non-profit "abortion boat" docked on its shores.