Only four per cent of the crop was eradicated and two per cent of the harvested product was seized.
The West has long said that money from the drugs trade funds the Taliban and fuels corruption and crime in Afghanistan, weakening the state it is attempting to support.
Afghanistan has long been the producer of about 90 per cent of the world's opium, a thick paste from poppy that is processed to make heroin.
In 2007, it broke all records, but cultivation has since started to decline.
"The bottom is starting to fall out of the Afghan opium market. These results are a welcome piece of good news and demonstrate that progress is possible," said Antonio Maria Costa, the executive director of the UN Office on Drugs and Crime.
This year, 123,000 hectares were used to grow opium poppy, compared to 157,000 hectares in 2008, UNDOC said.
Helmand province, the main focus of US and British war efforts, saw the greatest reduction.
Cultivation there fell by a third to 69,833 hectares, from 103,590 hectares in 2008.
Despite the decline in cultivation, the amount of opium produced fell by only 10 per cent - farmers produced 6,900 tonnes of opium were produced in 2009, compared to 7,700 tonnes in 2008.
That is far more than the 5,000 tonnes the world's users consume, leading to a glut that has depressed prices to lows unseen since the 1990s.
"All of that has created stocks, an excess supply, and on the whole has driven conditions such that it has become less and less attractive for farmers to cultivate opium," Costa said.
The fall in price drove the total value of Afghanistan's opium crop down 40 per cent to $438m.
Costa cautioned it was "too early to tell whether the decrease in cultivation and production over the past two years is a market correction that could be reversed, or a downward trend".
With Afghanistan still producing more opium than the world can consume, there is a risk that massive stockpiles of the drug could fund instability for years to come.
"They don't know where that [stockpiled] supply is," James Bays, Al Jazeera's correspondent in Kabul, reported.
"They believe it is in a number of stashes, possibly buried underground, either in Afghanistan or a number of neighbouring countries."
Opium now makes up just four per cent of Afghan GDP, compared to 7 per cent in 2008 and a record 27 per cent in 2002, a year after the Taliban were ousted.