MAHMOUDIYA, Iraq—U.S. soldiers preparing for raids study maps, examine photos of wanted men and check their weapons. Starting next month, they’ll have to go see a judge.

For nearly six years, American troops have been free under a U.N. mandate to search any home and detain anyone deemed a security risk.

All that changes next month, when the mandate expires and a U.S.-Iraqi security agreement takes effect. From then on, troops must obtain Iraqi warrants for searches and arrests—and U.S. officers say the requirement is one of the biggest headaches in complying with the new rules.

“It takes away the option of saying, ’hey, this guy just came into town and we want him and we want him now,”’ said Capt. Tom Smith, a company commander on his second tour in Iraq. “For some of us who were here before, it feels a bit slow.”

U.S. troops are scrambling to learn the ins and outs of an Iraqi legal system with unfamiliar rules and procedures, a cumbersome bureaucracy and a shortage of judges after years of violence.

The Americans are having to turn to their Iraqi colleagues for help in navigating the system. They’re also trying to improve it, working with the Iraqi investigators to enhance their evidence-gathering techniques, such as the use of biometrics and forensics.

The Iraqi government began requiring its own security forces to obtain warrants after a series of offensives in the spring against Shiite extremists drew sharp criticism from rival political parties complaining their members were being unfairly targeted.

In recent operations, that has meant flying judges from Baghdad to targeted cities to expedite the process.

The U.S. military is about to face the same rules. The security pact states that as of Jan. 1, American troops may not search homes or make arrests without warrants “except in the case of active combat operations.”

That will be a big change for the U.S. military — one of several required under the security pact that allows the Americans to stay for three more years but imposes stricter oversight on their behavior.

The agreement was ratified by Iraq’s presidential council on Dec. 4, and U.S. and Iraqi commanders are now meeting to lay out guidelines for how the new rules will work on the ground.

U.S. soldiers—particularly special forces—have in the past staged raids without consulting the Iraqis when going after time-sensitive targets. Commanders have long been concerned about extremists infiltrating the Iraqi security forces.

“It’s a challenge and we’re working through it,” said Lt. Col. Jim Bradford, commander of the 1st Combined Arms Battalion, 63rd Armor Regiment from Fort Riley, Kan. “Warrants come from multiple locations and so we’re working through that as well.”

It’s not just the need for warrants that’s raising concern. It’s also the process.

To get a warrant in Mahmoudiya, troops will have to appeal to four Iraqi judicial investigators in the town, unless the Iraqi army brigade happens to have a warrant for the same individual.

Bradford, 39, of Lynchburg, Tenn., said his battalion began preparing for the shift shortly after taking over operations in Mahmoudiya last month. His soldiers are trying to match up their list of wanted men with those of the Iraqi security forces and obtain warrants before the end of the month.

“It’s just a matter of making sure that our warrants match their warrants and everything is correct,” he said. “They have been doing warrant-based operations since we’ve been here.”

Soldiers will need warrants not only for low-level insurgents but also so-called “high value targets,” meaning key figures in Sunni and Shiite militant groups.