The HMS Enterprise, which had been on a Mediterranean deployment evacuated 110 people, mostly British from the capital Tripoli, ambassador to Libya Michael Aron wrote on Twitter.
"A number of passengers were transferred to Enterprise by boat and given supplies for the journey," the ministry said in a statement.
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Britain is also planning to temporarily suspend its embassy operations in the troubled north African country, the Foreign Office said.
The operation today resembles one conducted in 2011 during the bloody uprising that ousted the dictator Moamer Kadhafi, when a Royal Navy ship evacuated foreigners.
Ambassador Aron has said he has "reluctantly" decided to leave due to the worsening local clashes.
"Fighting in #Tripoli worse today.Oil tanks hit again. Fighting in civilian areas. Ordinary people suffering. Militias destroying the city," he had tweeted yesterday.
Libya has suffered chronic insecurity since Kadhafi's overthrow, with the new government unable to check militias that helped to remove him and facing a growing threat from Islamist groups.
Fighting between the rival militias has forced the closure of Tripoli's international airport, while Islamist groups are battling army special forces in the eastern city of Benghazi.
In the past week, many countries have ordered their citizens to leave and, in some cases, have evacuated them.
Between 100 and 300 Britons are thought to be in Libya. Many British consular staff were evacuated last Monday.
"Fighting has intensified in Tripoli, including around the British embassy compounds," a Foreign Office spokesman said.
"In the light of the deteriorating security situation, we are taking steps temporarily to suspend operations at the British embassy in Tripoli after the planned assisted departure of British nationals," he said.
"We advise against all travel to Libya and urge British nationals in Libya to leave through commercially available means," he added.
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