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Pentagon sources say the helicopters were carrying elite US Army Ranger units on a mission to capture a local warlord in the east African state.
One US soldier is believed to have been taken hostage. In an earlier incident three marines were wounded and a Somali killed when a remote-controlled mine exploded under their vehicle.
'Vital humanitarian mission'
The deaths bring to 16 the number of Americans killed in combat in Somalia since the United States intervened in December last year.
President Clinton released a statement expressing his sympathy over the deaths of "brave Americans engaged in a vital humanitarian mission".
The helicopters were shot down at around 1545 local time yesterday (1245 GMT) at the start of an operation to take into UN custody members of a faction led by General Muhammad Aideed.
The Pentagon said about 20 members were arrested after an assault on a heavily armed compound, including a senior ranking associate of the militia leader.
US forces then came under unexpected and sustained fire throughout the capital from armed militias.
Heavy fighting is reported to have continued through the night and into the early hours of this morning.
It is understood the Rangers required reinforcements from among the 1,200 strong US rapid reaction force stationed at Mogadishu airport.
US military officials say the number of soldiers killed or wounded is likely to grow, as more information on casualties comes in.
The United States has been operating in Somalia as part of the UN humanitarian mission in place there since 1992.
The UN mandate has been to take appropriate action to establish throughout Somalia a secure environment for humanitarian assistance.
Serious concerns are being voiced in Washington about the precise nature of US involvement in the war-torn country, and how long any of its troops should remain there.
Defence Secretary Les Aspin has stated that US forces will not remain in Somalia longer than necessary. But speaking on CBS he cautioned:
"It's important not to withdraw in a way that, 18 months later, people will say, 'Well, it never made any difference'."
An estimated 90-minute lightning assault turned into a 17-hour desperate battle to escape a hostile city.
The final toll was 18 Americans and a UN Malaysian soldier dead, and around 90 wounded.
Between 350 and 1,000 Somali gunmen and civilians were believed killed.
Two hostages, including a US pilot, were released on 14 October.
The US withdrew from Somalia in March 1994, followed by full UN withdrawal in 1995 at a total cost of 147 fatalities.
Today much of Somalia remains in a state of feud, famine and economic collapse.
Analysts argue the UN's initial policy of "coercive peace enforcement" blurred the boundaries between international humanitarian and foreign aggressor.
The episode continues to influence US military and foreign policy.
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