The Democratic Presidential candidate was seen being escorted from the event at Ground Zero with some reports suggesting she had fainted.
In a statement a spokesperson said:
"Secretary Clinton attended the 11 September Commemoration Ceremony for just an hour and thirty minutes this morning to pay her respects and greet some of the families of the fallen.
During the ceremony, she felt overheated so departed to go to her daughter's apartment, and is feeling much better."
Clinton later left the apartment telling reporters: "I'm felling great."
The Presidential hopeful has been the subject of rumour surrounding her health, with rival Donald Trump fuelling that speculation by calling on her to make her medical records public.
She responded to the claims last week, saying: "I'm not concerned about the conspiracy theories, there are so many of them I've lost track of them. I pay no attention to them."
Clinton was among several high profile people attending the15th anniversary memorial of the attacks on the World Trade Centre.