KABUL, Afghanistan – The government of President Hamid Karzai on Sunday denounced a NATO-led night raid on a compound in Kabul that killed two men, accusing Western forces of violating agreements governing security in the Afghan capital.

The quarrel highlighted long-standing disagreements between the Afghan government and the U.S. military, which makes up the majority of the foreign force, over the use of night raids. Afghan officials say such raids often result in civilian deaths.

The incident also underscored jurisdictional disputes that are likely to arise as Western troops begin handing over security responsibilities to the Afghan police and army. NATO plans call for Afghan forces to take the lead in safeguarding the country by 2014, paving the way for the departure of most Western troops, who now number about 150,000.

A spokesman for the Interior Ministry, Zemari Bashary, said that an Afghan police general who aided the Western troops had been suspended, and that a colonel was also being interrogated about his role. An investigation was continuing, he said.

The NATO force said in a statement that Friday’s raid on the compound of a private Afghan security company came in response to what it termed a “credible threat” to attack the U.S. Embassy using explosives-laden vehicles. Some weapons were seized, but the search failed to turn up car bombs or materials for making them.

At a news conference, Bashary called the incident “tragic and unfortunate,” and said it violated a 2-year-old agreement that any security operations in the capital are to be cleared in advance, with Afghan police or soldiers taking the lead. “This shouldn’t have happened,” he said.

NATO said its forces were fired upon after announcing their presence at the compound, and returned fire. Two guards were killed, two were injured, and 15 people were taken into custody.

Afghan officials familiar with the incident said those inside the compound believed they were under attack by criminals or insurgents, and fired in self-defense. Those who were detained were freed after a senior Afghan military official arrived and vouched for them, Western officials said.