The project, Casa Heurtematte, will have several levels for offices, apartments and a cafeteria.
Photographs show that pillars violate constraints placed on projects in the area.
Sebastián Paniza, representative of the International Council of Monuments and Sites (Icomos) in Panama, points out that the seabed is state-owned, which would be a violation.
Hildegard Vásquez, executive director of the Calicanto Foundation, is concerned that, despite the allegations, regulations are not enforced.
Vásquez mentioned that a 2004 executive decree specifically states that development can not take place in the seabed.
In that sense, the activist said that the wall surrounding the area, which dates from 1688, has more importance than any building built after it.
She said the failure of the government to regulate the Plaza Independencia project has weakened its ability to regulate development in the area.
Javier Edwards, director in charge of Historic Heritage of the National Institute of Culture, said that he received images of the work and that he will order an inspection of the project to determine if he complied with the approved plans.
According to Edwards, it is necessary to evaluate if the original structure to determine if there was a violation.
José Díaz, the architect of the work, maintains that they have all "documents in order" and that the piles that rise near the sea line are part of the original structure of the building built in 1885.
"The project has the approval of the Directorate of Historic Heritage," he added.