The traditional land owners, the Larrakia people, have been asked to encourage the homeless to leave places on the president's program.
Larrakia Nation chief executive Ilana Eldridge says the "gentle suggestion" has come from the Northern Territory government.
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"When we go in, people know it is time to move, otherwise the cops will come in heavy-handed later," Ms Eldridge said.
"We take them to another place where they will be comfortable and safe and then in a few days time they will drift back."
NT Chief Minister Paul Henderson says Mr Obama's security is paramount and there will be exclusion zones around where he is travelling.
"This is one of the facts of life when the president comes to town," Mr Henderson told ABC radio.
"That happens everywhere in the world, not just here in Darwin."
Ms Eldridge believes there are about 2000 homeless people in the Darwin region each night, with 20 to 30 staying along The Esplanade, where Mr Obama will travel.
It's estimated about 95 per cent of Darwin's homeless population are of Aboriginal descent.
