Arizona Attorney General Tom Horne will file a lawsuit by week's end, asking a federal judge to weigh in on the legality of Arizona's Medical Marijuana Act and whether those who manufacture or distribute pot under the law are subject to federal prosecution.

Gov. Jan Brewer said Tuesday she directed Horne to file suit for "declaratory judgment" because of a letter written earlier this month by U.S. Attorney Dennis Burke. It is likely that she will put portions of the program on hold in the coming days, pending a legal ruling.

On May 2, Burke warned Arizona Department Health Services Director Will Humble that the state's new medical-marijuana law conflicted with the federal Controlled Substances Act and that "growing, distributing and possessing marijuana, in any capacity, other than as a federally authorized research program is a violation of federal law."

Burke added: "Compliance with Arizona laws and regulations does not provide a safe harbor, nor immunity from federal prosecution."

Brewer said Burke's words left her fearing for state employees, including those tasked with issuing dispensary licenses and qualified-patient and caregiver registration cards.

"I just cannot sit on the sidelines and allow the federal government to put my state employees at risk," Brewer said.

She added: "(That) letter really muddied the waters. ... I intend to get answers because peoples' lives and careers are at stake."

Burke's letter did not specifically mention state employees, but Brewer said it's clear they could be prosecuted.

Proposition 203, which legalized medical-marijuana use for people with certain debilitating conditions, was approved by voters in November and took effect April 14. The program is not yet fully up and running.

The Arizona Department of Health Services has issued more than 3,600 "qualified patient" cards and is scheduled to begin accepting dispensary applications June 1.

When asked whether she intended to instruct DHS to not issue dispensary permits, Brewer said, "we are moving in that direction."

Her spokesman, Matthew Benson, said later that the governor's advice to DHS on the subject was "imminent, in the next few days."

Brewer and Horne said Friday that they did not know how long it would take the courts to rule, and they would not take a position on the voter-approved law during the legal proceedings.

"We will not take a substantive position, either to thwart the will of voters ... nor to try to impose our own policy views," Horne said. "We are simply saying to the federal court, 'We need a resolution of these competing pressures.'"

Ryan Hurley, a partner at the Rose Law Group, which represents would-be dispensary owners, questioned the assertion that the suit was not political move.

"If they were in favor of protecting the voters' rights, they would be filing this action stating that the Arizona Medical Marijuana Act should be implemented," Hurley said, adding that his clients already have made a "significant investment" in their business.

Arizona is not the only state grappling with this issue.

Earlier this month, Rhode Island Gov. Lincoln Chafee halted the state's medical-marijuana dispensary program after the U.S. attorney for his district threatened to prosecute those involved with licensing "compassion centers" there.

There has been similar correspondence between federal prosecutors, attorneys general and governors in several other states, and dispensary and greenhouse raids in Washington, Montana, Colorado and California.

Republic reporter Mary K. Reinhart contributed to this article.