He told BBC Radio 5 Live's Breakfast programme: "It is always unfortunate to have these kind of protests for soldiers who have just come back from delivering the goods on the ground.
The Prime Minister condemned the protest, which saw two people arrested amid angry scenes as the 2nd Battalion The Royal Anglian Regiment paraded to mark their return from Iraq.
Gordon Brown praised the thousands of people who lined the streets of Luton, Bedfordshire, to show their support for the battalion, known as The Poachers.
But he expressed disappointment that a "tiny minority" of the crowd, who held up banners accusing the soldiers of being "cowards" and "extremists", tried to disrupt the event.
An Army spokesman said the battalion, which was due to take part in a similar march today in Watford, was "deeply touched" by the support despite the disturbance.
In a statement, Mr Brown said: "The whole country is proud of our brave servicemen and women who serve their country with great distinction and courage.
"That pride in our armed forces was shown once again today when thousands turned out to welcome the 2nd Battalion the Royal Anglian Regiment.
"It is therefore disappointing that a tiny minority tried, but ultimately failed, to disrupt today's event. We should all be proud of the outstanding work our armed forces do."
A group of Muslim protesters, who were hemmed in by police as the parade marched past, waved placards with slogans including: "Anglian Soldiers: Butchers of Basra" and "Anglian Soldiers: cowards, killers, extremists".
A number of people staged a counter-demonstration and Bedfordshire Police confirmed two people were arrested for public order offences and taken to Luton police station.
The protests were also condemned by Defence Secretary John Hutton and his Conservative shadow Liam Fox.
Mr Hutton said: "I want to pay tribute to the 2nd Battalion, The Royal Anglian Regiment who have served their country with great bravery and professionalism.
"I am grateful to the thousands of people from all walks of life that turned out in Luton today to offer their support and gratitude for the incredible job they do.
"I can only condemn the tiny minority who used this opportunity to make, whatever their personal views, utterly ridiculous and insulting comments to these brave men and women.
"I am extremely pleased to hear this has not in any way detracted from this proud day for the Poachers."
Dr Fox said: "This is offensive, appalling and disgraceful.
"It is only because of the sacrifices made by our armed forces that these people live in a free society where they are able to make their sordid protests."
Maj Gen Salmon, general officer commanding, Multinational Division (South East), was asked how the protest would affect soldiers in Iraq.
He said: "I think they would look at it, and say, that's just unfortunate, and I don't think it really affects what they understand as to what they have achieved themselves. I think they deal with it pretty pragmatically and maturely."
Asked what had been achieved, he said Iraqi people were saying: "We got rid of a dictator, it's been tough over the last six years, we are now in charge of our country, you've allowed us to stand on our own two feet."
It is time for the UK military mission to close down, but that would not be the end of the UK's long-term partnership with the people of Iraq, he said.
"This is a new mission, now, of advice and assistance," he said.