Guterres attributed the slowdown to major conflicts from Iraq to Afghanistan, Somalia or the Democratic Republic of Congo which showed no signs of abating.
"Persistent conflict in the Democratic Republic of Congo, Pakistan and Somalia mainly accounted for the increase in the overall figure"
UNHCR's Global Trends report
"Conflicts that had appeared to be ending or were on the way to being resolved, such as in southern Sudan or in Iraq, are stagnating. As a result last year was not a good year for voluntary repatriation," he said.
"In fact, it was the worst in twenty years," added the high commissioner.
Volker Turk, a UNHCR official, cited insecurity in Afghanistan in particular to explain the slowdown in repatriation of refugees.
Only 51,000 refugees returned to the country last year, compared to 275,000 in 2008, he said.
The total of 43.3 million forcibly displaced people in 2009 was the highest number since the mid-1990s, the UNHCR said.
"Persistent conflict in the Democratic Republic of Congo, Pakistan and Somalia mainly accounted for the increase in the overall figure," its Global Trends report found.
About one million refugees normally voluntarily repatriate every year, according to the UNHCR.
The world's overall number of refugees - defined as those who flee conflict or persecution across international borders - was stable last year at 15.2 million.
Burden on the poor
Developing countries were host to 80 per cent of those refugees, led by Pakistan with 1.7 million, Iran with 1.1 million and Syria with an estimated 1.1 million.
In addition to the 15.2 million refugees, there were also 27.1 million people internally displaced and another 983,000 people sought asylum in other nations.
South Africa received the largest numbers of claims for asylum, numbering more than 222,000 last year. That made up over a fifth of the nearly one million asylum claims last year.
The UNHCR provides humanitarian aid and protection to refugees, and helps broker resettlement in other countries where possible.
Afghan and Iraqi refugees account for nearly half of the refugees under the UNHCR's responsibility worldwide.
Over the last decade, at least 1.3 million refugees have been naturalised in another country, more than half of them in the United States.