It was already advising against travel to Somalia, including Somaliland, and now says any Britons in Somaliland despite its advice should leave.
It says kidnapping "motivated by criminality or terrorism" remains a threat throughout Somalia.
Last week, a similar warning was issued for Britons to leave Libya's Benghazi.
There were a number of non-governmental organisations, staffed by Westerners, that worked in Somaliland, a Foreign Office (FCO) spokesman told the BBC News website.
"We are now aware of a specific threat to Westerners in Somaliland and urge any British nationals who remain there against our advice to leave immediately," the FCO said in a statement.
It said it would not comment on the nature of the threat.
'Terrorist groups'
The FCO website warns that in the southern and central regions of Somalia "there is ongoing serious violence, dangerous levels of criminal activity and general internal insecurity".
It says attacks "could be indiscriminate, including in places frequented by expatriates and foreign travellers".
And it adds: "Following the death of Osama Bin Laden, terrorist groups operating in Somalia have made threats against Westerners and those working for Western organisations in Somalia, including Somaliland."
The northern territory of Somaliland broke away from Somalia in 1991 and wants to remain separate from the rest of the country.
But Mogadishu wants Somaliland to be part of a single Somali state.
Somaliland unilaterally declared independence after the overthrow of Siad Barre - who led Somalia's last functioning national government.
Last week, the FCO urged Britons to leave Benghazi immediately in response to a "specific, imminent threat" to Westerners.
Libya's deputy interior minister Abdullah Massoud responded by insisting the security problems in Benghazi did not warrant such a response.
The threat of terrorism in Africa was highlighted by a four-day siege at a gas plant near the town of In Amenas, in eastern Algeria, earlier this month which is believed to have left six British hostages dead.
Check the BBC website
I think the dirty south has started to infect the peaceful north with their terrorism
