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BAGHDAD, Iraq (CNN) -- Iraq's national security adviser has raised sharp questions about the way British forces handled the rescue of two of its undercover troops in Basra earlier this week and voiced concern about the infiltration of security forces by insurgents.

In London, Iraqi Prime Minister Ibrahim al-Jaafari discussed the "regrettable" incident with British Defence Secretary John Reid. Al-Jaafari said he did not know details of what happened but an inquiry was under way.

"We stand by the action of our forces on the ground. They did what they judged appropriate at the time and I commend their swift and decisive action in very difficult circumstances," he said in a statement.

Al-Jaafari stressed the row over the incident would not affect relations betwen Iraq and Britain.

Basra remained tense after a British armored vehicle escorted by a tank crashed into a detention center and soldiers later rescued two undercover troops apparently held by Shiite militia.

Five hundred people demonstrated in the city in protest at the British action and demanded an apology.

The dramatic operation Monday followed a day of rioting in the southern Iraqi city. Police and local officials said that was sparked when the two soldiers fired on an Iraqi police patrol.

National Security Adviser Mouwafak al-Rubaie told CNN it was "a most unfortunate" incident.

"It is a serious violation of sovereignty if MNF has raided a police station," al-Rubaie told CNN in a phone interview, referring to the multinational forces.

Two people in Arabic-style clothing, in a car and heavily armed, had been arrested by police because they could not verify their identity as British soldiers.

"They were taken to the police station and kept in custody to verify their identity," said al-Rubaie.

The Interior Ministry contacted the Basra governor to release the two detainees because they had received confirmation that they were British soldiers and there were negotiations to secure their release.

There the Iraqi and multinational versions of the story diverge, al-Rubaie said.

"The multinational forces said when they arrived at the police station the soldiers were moved to the private residence of a militia leader.

"Our story is that this is an annex to the police station and used for detaining people, hence the British troops went into that location and freed them."

"We work together. Who is in charge here? We are saying that it is a violation of sovereignty if multinational forces have raided a police station," he said.

"We are investigating this, as the Iraqi government, and we would like to find out what went wrong, obviously there was a failure of communication, we need to work on how we can avoid this in the future."

He also called for undercover operations by multinational forces to be regulated.

The incident also points to concern about the relationship police forces have about infiltration by outsiders, including insurgents and militias. (Full story)

"We are more concerned about the penetration by the insurgents and the terrorists," said al-Rubaie.

"We have a very scrupulous, very meticulous vetting procedure to prevent insurgents and terrorists from penetrating the ISF (Iraqi Security Forces)," al-Rubaie said.

British troops launched the rescue about three hours after Iraqi authorities informed British commanders the men were being held at the police department's major crime unit.

The British commanding officer in Basra said his fears for the arrested men increased after he received information they had been handed over to "militia elements."

The British military entered the police station Monday and a Warrior armored vehicle crashed through the perimeter wall of the jail.

When it was discovered the two men were not in the jail, they were rescued from a nearby house, Brigadier John Lorimer said.

Lorimer added that it was of "deep concern" the men detained by police were later handed over to Shiite militia.

Iraqi police said members of Iraq's Mehdi Army militia engaged the British forces around the facility, burning one personnel carrier and an armored vehicle.

Video showed dozens of Iraqis surrounding British armored vehicles and tossing gasoline bombs, rocks and other debris at them.

Reid told Wednesday's news conference: "There has not been a fundamental breakdown in trust between the British government and the Iraqi government.

"There has been an incident in which we took action to safeguard our soldiers. That incident will be investigated by the Iraqis and by a special investigation branch.

"I stand by the action that was taken but that should in no way diminish the fact that in Basra province, and indeed throughout Iraq, in the vast majority of exercises that are now being taken against counter-insurgency, Iraq forces are working shoulder-to-shoulder with the British and multinational forces there."

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