It said popular uprisings in Tunisia and Libya prompted more people to flee last year, including sub-Saharan migrants working in North Africa, after tighter border measures sharply reduced arrivals in Europe in 2009 and 2010.
"This makes 2011 the deadliest year for this region since UNHCR started to record these statistics in 2006," Sybella Wilkes, spokeswoman for the U.N. High Commissioner for Refugees, told a news briefing.
The UNHCR toll is an estimate that includes people of 15 nationalities known to have drowned or gone missing in the Mediterranean Sea, which divides Europe and Africa.
More than 58,000 people arrived in Europe by sea last year, also a record, including 56,000 who landed in Italy, half of them Tunisian, Wilkes said. Malta and Greece received 1,574 and 1,030 people, respectively, by sea.
"Most were migrants, not asylum-seekers," she said.
In addition, 55,000 "irregular" migrants crossed the land border between Greece and Turkey at Evros last year, according to Greek government figures.
Last April and May, armed forces loyal to then-Libyan leader Muammar Gaddafi forced migrants onto boats which they often had to skipper themselves in harrowing conditions, said Wilkes.
Despite high seas and poor mid-winter weather, three boats are known to have attempted the perilous journey from Libya already this year, one of which went missing at sea with at least 55 people on board after raising the alarm, Wilkes said.
Libyan coast guards have told the UNHCR that 18 bodies have washed up in the past week, including a dozen women and a baby girl, most of whom were Somalis living in Tripoli, she said.
Italian, Maltese and Libyan authorities were making efforts to rescue boats in distress in the Mediterranean. But the UNHCR renewed its call for all ships to carry out their duty of rescuing vessels in distress, in line with international law. (Reporting by Stephanie Nebehay; Editing by Mark Heinrich)