The remarks provoked an angry response in the Netherlands, which has more than 1,500 troops in Afghanistan, with the Dutch government summoning the US ambassador to explain Gates' comments.
The interview came a day after the US agreed to send an extra 3,200 marines to Afghanistan, after failing to convince Nato to send more soldiers.
"Most of the European forces, Nato forces, are not trained in counterinsurgency. They were trained for the Fulda Gap," Gates told the LA Times.
He was referring to a region in Germany where, during the Cold War, Western allied believed the Soviets could stage an invasion.
"Our guys in the east ... are doing a terrific job. They've got the thing down pat. But I think our allies over there -this is not something they have any experience with"
US Defence Secretary
Gates also contrasted Nato's experience in southern Afghanistan with what he said was the success of a US counterinsurgency programme in the east under army Major-General David Rodriguez.
"Our guys in the east, under General Rodriguez, are doing a terrific job. They've got the thing down pat," Gates said.
"But I think our allies over there - this is not something they have any experience with."
The US marine reinforcement will increase the US troop presence by about 10 per cent, from 27,000 to about 30,000.
Currently, there are about 26,000 US troops in Afghanistan, most of them serving under the 40,000-strong Nato-led International Security Assistance Force (Isaf).
Nato troops deployed to southern Afghanistan include forces from Britain, Canada and the Netherlands where they have faced a number of attacks by a resurgent Taliban and their supporters.
Jaap de Hoop Scheffer, Nato's secretary-general, defended the troops fighting in the south.
"I have the greatest respect for what the allies are doing in the west, the north, the east and the south," Scheffer, a Dutchman, said at the Nato headquarters in Brussels.
Nico Geerts, the Dutch contingent's commander in Afghanistan, also criticised Gates' comments in an interview with Netherlands public radio, saying that Dutch soldiers were "doing an excellent job".
PJ Crowley, a senior fellow at the Centre for American Progress, told Al Jazeera that Gates' comments looked as though he wanted to shift US priorities to Afghanistan.
Crowley said: "The US has to decide how important Afghanistan ultimately is.
"To the extent that Gates questions whether EU troops have the ability to do this, that makes it incumbent on the US to increase its troop presence beyond the 3,000 that Gates announced."
Crowley said that if Gates was putting greater emphasis on Afghanistan, then he was "at odds with what the chairman of the US joint chiefs of staff [Admiral Mike Mullen] said last month - he said Iraq is the major war we are facing".
In an attempt to defuse the row caused by the interview, the Pentagon said on Wednesday that Gates had not meant for his words to be interpreted as criticism of individual countries.
Geoff Morrell, a Pentagon spokesman, said Gates was saying that Nato as a whole was not structured to handle insurgencies.
"The secretary of defence has read the article and is disturbed by what he read," Morrell said.
"The totality of the piece leaves the impression that the secretary is disturbed with the performance of individual countries in Afghanistan. He is not."