The 32-member team visited a hospital as well as a school housing some 10,000 displaced people in Monrovia's New Kru Town quarter and then left for a refugee camp for Sierra Leoneans outside the city.
But it was turned away from the camp by troops loyal to President Charles Taylor.
Liberian Defence Minister Daniel Chea later played down the incident, saying the team was sent away because they were supposed to have met him before proceeding to the camp.
Liberian police and pro-government militiamen fired shots in the air in Monrovia's port area to break up a thousands-strong pro-US crowd as the military experts headed back to the city after being turned back.
Later, the US team resumed its mission after talks with the Liberian government and visited Monrovia's Samuel Kanyon Doe sports stadium, where some 25,000 displaced people are sheltered in abysmal conditions.
Thousands of Liberians cheered the US team, travelling in a convoy of 10 four-wheel drive vehicles, screaming support for Washington and urging Bush to send more troops to Liberia, founded by freed American slaves in the 19th century.
"I am sure that George Bush will not abandon us."
Philip, a displaced youth
"We want peace, we want Bush!" they shouted, flashing victory signs. Others shouted slogans against Taylor.
Philip, a displaced youth, said: "The arrival of the Americans is a good sign. Now we can return to our homes. I am sure that George Bush will not abandon us."
Bush vague on US peacekeepers
Meanwhile, Bush began his first official tour of Africa in Senegal on Tuesday, pledging help to end the Liberian war without stating whether he would commit troops in a proposed peacekeeping force.
He told reporters in Dakar that he had discussed Liberia with Ghana's President John Kufuor, the current head of the 15-nation Economic Community of West African States (ECOWAS) which is trying to broker peace in Liberia.
"I told him we would participate with ECOWAS. We are now in the process of determining the extent of our participation ... to maintain the ceasefire and to allow for a peaceful transfer of power," Bush said.
Bush with Senegalese President
Speaking at an infamous slave camp off the coast of the Senagalese capital Dakar, the US leader commented on his nation's dark past involving slaverey.
Although not apologising, Bush called slavery, "one of the greatest crimes of history."
"Christian men and women became blind to the clearest commands of their faith and added hypocrisy to injustice. A republic founded on equality for all became a prison for millions," he said.
He said African slaves had helped awaken the American conscience through their struggle for freedom and that "the very people traded into slavery helped to set America free."
Bush added that the United States would stand with Africans to advance economic and political freedoms.
"Against the waste and violence of civil war, we will stand together for peace," he said.