Frazer, the highest ranking US diplomat to visit Somalia since 1993, had originally planned the trip for January but it was called off due to security concerns.
She urged Somalia to focus on reconciliation and end 16 years of conflict.
Frazer said: "Somalia, unfortunately, has become a haven for terrorists, and that continues to be a prime concern of the United States of America."
Hussein Mohammed Noor, a Somali analyst, told Al Jazeera: "I think if Mrs Frazer wants to achieve a peaceful situation in Somalia, she can do it, because America has the capacity."
But he said Frazer should not just be meeting members of the transitional government.
"She should stand an equal distance from all the parties. The Somali people at present believe America is not fair, or not neutral," Noor said.
War crimes fears
Earlier, an EU conflict expert warned that Ethiopian and Somali forces may have committed war crimes during heavy artillery shelling in the capital, and that foreign donors could be complicit.
"I need to advise you that there are strong grounds to believe that the Ethiopian government and the transitional federal government of Somalia and the African Union [peacekeeping] Force Commander, possibly also including the African Union Head of Mission and other African Union officials have through commission or omission violated the Rome Statute of the International Criminal Court," he said on Friday.
"The situation is Somalia has gone from bad to worse after the intervention of Ethiopian troops"
Abed, Kumasi, Ghana
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The warning was made in an email to Eric van der Linden, the chief EU official for Kenya and Somalia.
A Somali human-rights organisation has said that more than 1,000 civilians were killed or injured during the clashes with local militias.
"The European Commission is now very concerned about any allegations of war crimes and they are going to look into those alleagtions themselves," Tom Porteous, director of Human Rights Watch, said.
"... if it does emerge that the transitional government and the Ethiopians have committed war crimes then that would be very embarrassing for the European Union which has been funding the transitional government and the Ethiopians." Reconciliation conference
Meanwhile, Somalia's foreign minister announced that a reconciliation conference planned for April 16 has been postponed until May.
Ismail Mohamed Hurre also told a pan-Arab newspaper that the Union of Islamic Courts, which controlled much of central and southern Somalia until late December, would not be invited to the delayed conference.
He told Asharq Al-Awsat
there was "no question of any involvement of or participation by the Islamic courts.
"When we arrive at a constitutional phase, they can found a political party."
Somalia needs around $42.2m to organise the conference, but some potential donors have made aid conditional on moderate Islamists abeing invited.