All Somali visitors and refugees arriving in Uganda are to be registered in response to militants threatening to attack the capital, Kampala.
Somali community leaders living in Kampala said they would help to root out any insurgents.
It comes after al-Shabab said they would attack Kampala because Ugandan soldiers were serving with the African Union peacekeeping force in Somalia.
Islamist insurgents control much of southern and central Somalia.
In the capital, Mogadishu, they are fighting for control with troops loyal to the government, which is backed by UN and AU peacekeepers.
Numerous threats
The BBC's Joshua Mmali, in Kampala, says many Somalis in Uganda have unclear refugee status, so fear any unwanted attention.
They believe an al-Shabab attack on Kampala would lead to indiscriminate arrests in search of the perpetrators.
map showing areas under Islamist control
Following the threat by al-Shabab, Somali elders met Ugandan security officials to discuss combating the threat.
"We are ready to help the government to report any movement of these people," said Abdulaye Hassan Roble, a Somali community leader in Uganda.
"If they [al-Shabab] appear here in Uganda we shall report them to the government."
Al-Shabab also threatened to attack Burundi's capital Bujumbura because their soldiers are also deployed in Somalia.
It comes weeks after al-Shabab fighters also threatened Kenya after accusing its government of recruiting troops to fight for the Somali government.
Somalia last had a functioning central government in 1991.
Since then numerous armed groups have been fighting for control.
Islamist rebels who are accused of having links to al-Qaeda dominate much of southern and central Somalia, while the government runs only parts of the capital, Mogadishu.
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