Border Patrol officials have pulled thousands of rifles from field agents in a large-scale effort to refurbish the weaponry, prompting the rank-and-file to complain that they've been left with the dangerous options of sharing guns or being disarmed altogether.

Nearly one-third of the U.S. Customs and Border Protection's 16,300 M4 carbine rifles were tested by the agency's office of training and development, which determined that more than 2,000 had the potential for malfunction. The rate of nearly 40 percent was "more than we are comfortable with,” said CBP Deputy Chief Ron Vitiello.

"Our top priority is to make sure our agents are safe,” said Vitiello, adding that the agency intends to eventually cycle through all of the rifles to ensure that those in need of repair are fixed. “They will be like new when they are refurbished.”

But in the meantime, Border Patrol agents are dubious about the department's claims, given that the guns' manufacturer, Colt, has not issued a recall. And they are vehemently opposed to "pool guns" -- weapons shared by two or more agents.

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“We’d like to know why the rifles were recalled and when they will be returned,” Shawn Moran, spokesman for National Border Patrol Council, the union which represents agents, told FoxNews.com. “Our agency is trying to figure out why they were pulled."

The M4 carbine is one of several rifles derived from the M16. It is shorter and lighter than the M16, is powered by a gas impingement system and can fire 5.56×45mm ammunition in three-round bursts. Already heavily used by the U.S. military, the M4 will eventually replace the M16. Although Colt was the original manufacturer, versions are now made by such gunmakers as Bushmaster and Remington.

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Moran said there is potential danger for agents relying on rifles shared with others, noting the importance of personalizing settings and having a general familiarity with a personal weapon.

“You don’t want a weapon that is zeroed in to someone else,” he said. “You don’t share guns and you don’t share needles because both could end with people dying.

“We work in areas and situations where having these rifles could be a matter of life or death,” he added.

Customs and Border Protection officials said the scrutiny of the M4 carbines throughout the nation's Border Patrol sectors will continue until all have been inspected and, if necessary, repaired or replaced. He defended the use of pool guns to ensure each sector's armory was stocked.

But the agents' concerns are valid, one law enforcement expert told FoxNews.com.

“They are losing 40 to 50 percent of their M4s," said Jeff Prather, a former Drug Enforcement Administration agent who now runs the Warrior School, an independent law-enforcement training facility in Tucson. "They are basically disarmed.”

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Agents already risk being outgunned on the border, where powerful cartels are entrenched and armed to the teeth, said Prather, adding that agents have privately expressed their concerns to him.

“If they are less prepared, they are going to be less inclined to engage,” Prather said. “It’s a real concern, especially if they are telling me about it.”

Prather, who used the M4 throughout his law-enforcement career, said the weapon is “very robust” and that any issues found in the Border Patrol inspections are likely simple fixes.

“All you need to do is pull out the old firing pin and put in the new one and the rifle is ready to go,” he said.

Vitiello said that may be the case, but the work must be done by a specialist.

“It may be easy to replace a firing pin, but these are things that should be done by a professional,” he said.