Carolina Borges told sports newspaper A Bola that she might still have competed if she had received more support from the team mission.
"I am three months pregnant," she said. "I am saddened, (but) imagine if I broke something while I am pregnant, how would it be?"
"I never got any subsidies or moral support. I went ahead with the decision to quit because I lacked support," she added. "If I had had the support of a coach, things would have been different and I would have risked competing."
The Portuguese mission dismissed the allegations, writing in a statement emailed to Reuters that Borges "deliberately concealed the pregnancy".
The national Olympic committee said Borges did have a coach, shared with others in her class, and that she had received Olympic funding, albeit with a delay because she provided the wrong banking details.
"This was a total surprise to us," the mission wrote. "The athlete is contractually obliged to report to us all her clinical situations, which she never did.
"Given the obvious lack of compliance by the athlete, the contradictions in her statements and the assumed deliberate omission of the pregnancy, there is nothing the Portuguese Olympic mission can be blamed for."
Brazilian-born Borges, 33, represented Brazil at the Athens Olympics in 2004 but later joined Portugal's squad.
She lives in Miami and is married to U.S. sailor Mark Mendelblatt, who is competing in the Star class in the sailing regatta on the south coast of England.