"My special prayer goes to those who died here and may their death bring unity to the world," the President said.
She was accompanied to "Ground Zero" by husband Jose Miguel Arroyo, daughter Luli and son Diosdado, some senators and other members of her official party.
They were joined by New York Mayor Rudolph Giuliani who expressed gratitude for the visit.
Mrs. Arroyo said as a result of the attacks on the WTC and the Pentagon in Washington DC which left some 5,000 dead or missing, former adversaries like China, Russia, Iran were one in condemning the atrocities.
She said world trade collapsed after the WTC went down and world trade would recover as the WTC is revived.
Mrs. Arroyo, who stayed at the site for about an hour, reiterated that the Philippines joined the international fight against terrorism being spearheaded by the United States.
She recalled that her family had their pictures taken at the WTC during previous visits to New York.
She said they always had cocktails at the restaurant at the top of the building called "Windows of the World."
"Now it’s all gone," she lamented.
For his part, the First Gentleman also expressed sorrow over the tragedy and offered prayers for the victims.
Security was tight at Ground Zero, with police allowing only authorized vehicles to enter after rigid screening. – With PNA