This is the largest such influx since UNHCR began compiling these statistics in 2006. The previous record high was in 2011, when more than 103,000 people arrived in Yemen on smugglers' boats.
Some 84,000, or more than 80 per cent, of the arrivals were Ethiopian nationals, while Somali refugees constituted the rest.
Many migrants use Yemen as a transit stop en route to states in the Persian Gulf, the agency said in a press statement from Geneva Switzerland.
Despite economic and security difficulties last year, Yemen continued to receive and host a record number of people fleeing the Horn of Africa in search of safety, protection and better economic conditions.
All Somali arrivals are automatically recognized as refugees by Yemeni authorities.
UNHCR conducts refugee status determination for Ethiopians and other nationalities seeking asylum in Yemen.
A very low percentage of Ethiopian arrivals decide to seek asylum, either due to a lack of awareness and access to asylum mechanisms or because they do not meet the criteria to be recognized as refugees.
However, for the vast majority of Ethiopian migrants protection space is nearly non-existent and they are often extremely vulnerable.
In Yemen, staff from UNHCR and its local partners conduct daily patrols along the Gulf of Aden coast to provide assistance to all new arrivals that pass through strategically positioned reception and transit centres.
However, there are substantial difficulties in responding to the various protection risks that new arrivals face in transit and upon
arrival in Yemen.
Boats crossing to Yemen are often overcrowded and smugglers, in order to avoid the Yemeni coastguard, sometimes force the passengers into the water, often far from the shore and in stormy weather.
UNHCR estimates that at least 100 people have drowned or gone missing while trying to cross the Gulf of Aden or the Red Sea in 2012.
New arrivals are at risk of exploitation, violence and sexual abuse.
The situation is particularly difficult along the Red Sea coast, where Yemeni smugglers and traffickers are often waiting to receive new arrivals. Traffickers mainly target Ethiopians looking to travel onwards to Persian Gulf states.
Conflict and instability in the north and south of the country has curbed the ability of Yemeni authorities to address trafficking. In 2012, there was a proliferation in smuggling and trafficking and a significant increase in reported cases of violence and abuse
perpetrated against new arrivals. The increased presence of armed gangs of smugglers and traffickers is an additional risk to aid workers.
'The continually growing mixed migration movement from the Horn of Africa is an issue affecting the region beyond Yemen,' UNHCR spokesman Adrian Edwards said in Geneva on Tuesday.
'We welcome the decision of the authorities in [the Yemen capital] Sana'a to host a regional conference this year with UNHCR as part of wider efforts to develop a strategy to manage the flow of mixed migrants, and prevent and reduce smuggling and trafficking in the region.'