Clinton left at around 9:30, but her team did not confirm why she had been driven away until 11am.
Onlookers have also said her symptoms seemed far worse than her aides have suggested.
Merrill said in a statement: ‘Secretary Clinton attended the September 11th 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.’
When she was taken away, she had to wait for a couple of minutes for her motorcade as it wasn’t waiting for her, witnesses said.
Fox News reporter Rick Levanthal said one person standing 15ft away from her told him her knees buckled as she stepped off of a curb.
She also appeared to lose a shoe as she walked into the vehicle.
Her detail retrieved a shoe from underneath the van and helped the former Secretary of State inside, according to reports.
The temperature was around 80 degrees at Ground Zero during the service.
Clinton was standing in the middle of a crowd of politicians packed together in a small space.
It is not known if she was standing in direct sunlight. There are many shaded areas surrounding the memorial.
Clinton suspended campaigning on Sunday in a show of support and respect for both those who died and those who survived the attacks.
The latest reports will add to claims from conspiracy theorists she has health problems.
Right-wing groups have tried to suggest pictures of her being helped a long by her security detail prove she is ill.
Controversial blog, American Mirror, started its conspiracy-theorizing post by stating Clinton’s health should be ‘a major issue of the 2016 campaign’.
Dr. Drew Pinsky’s HLN show was brought to an end after he made bizarre claims Clinton is suffering from a wide range of health problems, including brain damage.
He made the claims despite an extensive review revealed of her records revealed she was in good health.
Before the anniversary, Clinton recounted her memories of that fateful day that left 2,977 people dead.
She was serving as Senator of New York at the time and was heavily involved with dealing with the horrific aftermath.
In an interview with CNN’s Chris Cumomo, she said: ‘We saw this curtain of black smoke that was stretched across the island.
‘Occasionally it would be broken by a firefighter coming out. I remember one image so indelibly, dragging his ax, and it was as close to depiction of hell that I’ve ever personally seen.
‘There weren’t that many survivors; the ones that did survive were grievously injured. The loss of life was overwhelming.
‘But it was also my job and the job of other officials to get our city and state and country what we needed.’
Source : Daily Mail