“While we are not at liberty to disclose the specifics of these confidential personnel matters, we wanted you to be aware of this before the start of rehearsals,” on Tuesday, wrote Mr. Stafford, who is likely to be in the running for the post of artistic director — a reimagined version of Mr. Martins’s job of ballet master in chief.

Some in the company have questioned whether this week’s punishments are a reaction to the tumultuous departure of Mr. Martins. One dancer, who requested anonymity because company members are not authorized to speak on the matter, described the organization’s abundance of caution as a wild swing of a pendulum from the culture of Mr. Martins’s tenure, adding, “Everything is under more scrutiny than ever.”

Casting for the coming season has not been posted, but the absence of these three dancers will send ripples through the schedule. Mr. Ramasar, whom the New York Times critic Alastair Macaulay has called “an endearing and central artist,” has been away from the company since earlier this year to perform as Jigger in the Broadway revival of “Carousel,” which ends its run on Sept. 16. (He is also scheduled to dance with his frequent City Ballet partner, the principal Tiler Peck, in a premiere at this year’s Fall for Dance Festival.)