Lieutenant General Ricardo Sanchez said in Baghdad on Tuesday the number of foreign resistance troops was "probably a couple of hundred".
The announcement comes in stark contrast to comments made on Monday by US-led occupation administrator, Paul Bremer.
Bremer told The Times of London he believed resistance was set to increase, as large numbers of professional fighters continued to move into Iraq each week.
Sanchez also confirmed the detention of 20 men thought to have ties with Usama bin Ladin's al-Qaida organisation, which according to his calculations would equal 10% of the "foreign threat".
Occupation troops in Iraq face
20-30 attacks daily
Sanchez said Yemenis, Sudanese, Syrians and Egyptians were among the detainees, but stressed all were still under investigation and had not been proven guilty of anything.
But the lieutenant general added the prisoners, even if they were not al-Qaida, had possibly received some financing and training from other "international terror groups".
With an estimated 25 to 30 resistance operations against US-led occupation forces daily, Sanchez's statement puts into perspective the limited nature of any al-Qaida threat in Iraq.
In an exclusive interview with Aljazeera.net, a strategic studies researcher based in Baghdad University confirmed that the majority of attacks were being carried out by Iraqi nationalist and Islamist groups.
"It is important to mention nationalist resistance - among the dead we have found Turkmen and Iraqi Christians as well as Muslims"
Salman al-Jumaili, doctor of political science at Baghdad University, is researching the backgrounds of resistance fighters killed in combat.
His studies reveal the vast majority of them are Iraqi Muslims - Sunni and Shia - who are fighting for the sole purpose of pushing America out of Iraq.
Al-Jumaili's analysis of resistance casualties and fatalities has led him to the conclusion that "Saddam loyalists" or al-Qaida do not feature in any major role at all.
It is more appropriate, he says, to describe resistance in Iraq as Islamic and nationalist.
"It is important to mention nationalist resistance - among the dead we have found Turkomans and Iraqi Christians as well as Muslims."
Although Iraqi Islamist fighters form the great majority of the resistance, no particular group predominates, he says.
There are literally dozens of militias with no central planning or coordination, although there is some evidence to suggest a few Islamist groups have began to coalesce in recent weeks.
"There are many differences between the different groups, even between different Islamist resistance forces, but the unifying cause for the struggle is the American occupation."