Although attacks decreased in September during the Muslim holy month of Ramadan, July and August saw the highest number of clashes since 2002, an increase of up to 40 per cent compared to the same period last year, Eide said.
Just hours before Eide gave his report at least nine people were killed when a bomb exploded as their minibus passed in Uruzgan province.
But Eide also emphasised positive developments in Afghanistan, including improved relations with neighbouring Pakistan, the appointment of an interior minister committed to rooting out corruption and a 19 per cent drop in output in opium producing regions.
Zahir Tanin, Afghanistan's UN ambassador, echoed Eide's fears saying: "Despite hard work on the part of international coalition forces and Afghans alike, terrorism appears to be on the rise again.
"The Taliban burn down schools, stamp out reconstruction, and butcher civilians," he said.
"They attack roads and regions around Kabul, hampering international humanitarian relief. Ordinary people are increasingly their targets."
However, he also cautioned against overly pessimistic reports about the situation in his country because such statements were used by the Taliban to convince Afghans of wavering international support.
"We should be careful with what we say about Afghanistan," Tanin said. "Media outlets move with astonishing speed in Afghanistan and word of mouth carries any pessimistic news quickly to the Afghan people."
Earlier this month, in comments widely reported in Afghanistan, Brigadier Mark Carleton-Smith, the British commander in Helmand province, told a newspaper that the war against the Taliban could not be won.
Zalmay Khalilzad, the Afghan-born US ambassador to the UN, said on Tuesday that success was still possible in Afghanistan but hinged on more than military objectives.
He said Kabul must combat corruption, enforce the rule of law, achieve economic development, fight the drugs trade, reform the police and hold a general election in 2009.