Federal agents swarmed the Menominee Indian tribe's Wisconsin reservation Friday and eradicated 30,000 cannabis plants, confusing and alarming tribal leaders, policy reformers and attorneys who work with other American Indian tribes considering growing marijuana or hemp.

Menominee leaders say the plants were intended for lawful research into growing industrial hemp, which is processed and utilized for fiber, food and oil and is distinguishable from marijuana by its lower levels of the high-inducing compound tetrahydrocannabinol (THC).

Growing hemp was illegal in the U.S. for decades until an amendment to the 2014 federal farm bill allowed states to implement pilot programs growing hemp for academic or agricultural research. Several states, such as Colorado and Kentucky, have done so, and the Menominee announced earlier this year they would, too, in cooperation with the College of the Menominee Nation.

The Drug Enforcement Administration and acting U.S. Attorney Gregory Haanstad contend the seized plants were in fact marijuana, but a search warrant affidavit filed last week by a DEA agent does not identify a specific THC level as grounds for the search-and-seizure operation.

The affidavit says the tribe consented to a member of the Bureau of Indian Affairs visiting to sample and test cannabis plants. In addition to witnessing "individuals appearing to be non-native" and a Colorado-based consultant aiding the tribe, the affidavit says samples taken tested positive for the "presumptive indication" of marijuana.

Initial testing of the samples – done using a Narcotics Analysis Reagent Kit – were negative. The affidavit theorizes that was due to the field testing kit being stored in a vehicle. A retest using a different kit, the affidavit says, resulted in positive tests.

It's unclear if subsequent lab testing has been or will be performed. Accurately testing cannabis samples for THC levels is notoriously difficult, and the precise THC level is the key detail that distinguishes marijuana from hemp.

In states that require testing of compounds in commercial cannabis, labs generally use ultra performance liquid chromatography that requires complex and expensive machines that must be painstakingly calibrated for accuracy.

THC levels aside, defenders of the tribe point to the Justice Department memo that last year gave federally recognized tribes a green light to legalize marijuana for recreational use, so long as they do not trip certain enforcement priorities established in 2013 for states, such as engaging in organized crime, disseminating marijuana to other jurisdictions or providing it to minors.

Robert Odawi Porter, a tribal law expert and former president of New York’s Seneca Nation, says “this certainly suggests a real divergence in policy approach for Indian country” compared to states, which have been allowed to regulate massive seed-to-sale recreational marijuana marketplaces.

“It increasingly looks like the Justice Department guidelines are not being interpreted in the same way as they were intended,” says Porter, who in February helped host a large cannabis-focused conference for tribal leaders.

Lance Morgan, another prominent tribal law expert, agrees the guidelines are not being applied consistently by the Justice Department.

Morgan, a member of Nebraska’s Winnebago tribe, has worked with tribal governments considering cannabis reform and says the raid likely will be remembered as a historic betrayal.

“How can you allow people to buy marijuana in a retail environment in some states and then raid an industrial hemp operation of a tribe? The only difference is that there is a tribe involved,” he says. “This odd federal policy of encouraging investment and then raiding the new business sets us back a few decades in federal tribal trust and economic policy.”

Morgan anticipates the raid drying up investment in tribal cannabis ventures.

“The new federal policy of ‘sort of’ allowing tribes to get into the marijuana business is especially cruel and unusual because it encourages investment, but after the investment is made the federal government comes and shuts it down and the investors lose all their money,” he says.

The Menominee raid isn’t the only indication that the Justice Department and the DEA are cracking down on tribal experiments with cannabis. In July, two California tribes – the Pit River Tribe and the Alturas Indian Rancheria – were raided by federal agents who seized 12,000 plants. Alleged issues included financing from a foreign businessman and concern the marijuana would be distributed off tribal land in a manner inconsistent with California’s lenient medical marijuana law.

In another bad omen for reformers, the U.S. attorney for South Dakota in June refused to agree to lifting a court order banning Alex White Plume of the Oglala Sioux Nation from farming hemp, the growing of which his tribe legalized. Plume had in the early 2000s engaged in acts of hemp-growing civil disobedience, resulting in the order.

Eric Steenstra, president of the advocacy group Vote Hemp, says “our sense is that the Justice Department as a whole has lurched in a bad direction.”

“It’s not like [the Menominee] were doing a clandestine marijuana grow, they told them up front what they were doing,” he says. If the THC content was high, it may not be the tribe’s fault, he says, given difficulty in procuring seeds for particular strains after decades of prohibition.

“We’re definitely frustrated and disappointed,” says Steenstra, adding that his group may lobby allies in Congress to sponsor an amendment that would protect tribal autonomy. A similar measure was incorporated into a large spending bill after the DEA impounded an order of hemp seed destined for Kentucky’s state government last year.

Former U.S. Attorney for North Dakota Tim Purdon is working with the Menominee tribe and blasted the raid as a "waste of resources" that "is exacerbated by the fact that the Tribe had agreed to act itself to destroy individual strains of the hemp crop that the Tribe and the U.S. Attorney’s Office agreed were problematic.”

“This misallocation of federal resources is exactly what the [2013] Cole and [2014] Wilkinson Memos were designed to prevent,” he said, referring to the Justice Department memos allowing states and tribes, respectively, to regulate marijuana.

Purdon, now a partner with the law firm Robins Kaplan LLP, and an official with the Menominee tribe declined Monday to discuss their plans to respond to the raid, but hinted at a possible lawsuit in an initial statement.

In that statement, Menominee Tribal Chairman Gary Besaw blasted federal agents.

“I am deeply disappointed that the Obama administration has made the decision to utilize the full force of the DEA to raid our Tribe,” he said. “We offered to take any differences in the interpretation of the farm bill to federal court. Instead, the Obama administration sent agents to destroy our crop while allowing recreational marijuana in Colorado. I just wish the President would explain to tribes why we can't grow industrial hemp like the states, and even more importantly, why we don't deserve an opportunity to make our argument to a federal judge rather than having our community raided by the DEA?”

The tiny Flandreau Santee Sioux tribe of nearby South Dakota, meanwhile, is preparing to serve recreational marijuana to outsiders on its resort, and tribal attorney Seth Pearman says the tribe has no plans to change course.

Pearman says "it would be shocking" if his tribe were to be raided by the DEA. "We've done the best we can to make a good system," he says.

The South Dakota tribe currently has a batch of month-old plants, Pearman says, and the tribe plans to welcome its first marijuana tourists around the end of December.

A Justice Department spokesman says there’s been no shift in policy. It’s conceivable that some local U.S. attorneys, who have had broad discretion to implement federal marijuana laws, which ban nearly all cannabis possession, simply are being more zealous than others, as has long been the case with federal medical marijuana cases.

“There has been no change in policy with respect to tribal sovereignty and the enforcement of federal drug laws,” says Justice Department spokesman Wyn Hornbuckle. “The Justice Department is committed to dealing with tribes on a government-to-government basis, consistent with the special trust relationship of the federal government to the tribes, and the federal government’s particular authority for law enforcement in Indian Country.”

Hornbuckle says, consistent with existing policy memos allowing states and tribes to regulate marijuana, “each United States Attorney has been directed to assess the threats and circumstances in his or her district and consult closely with tribal partners and the Justice Department when significant issues or enforcement decisions arise in this area.”

The Justice Department, he adds, “is still looking at the facts and circumstances surrounding this ongoing matter, so it would not be appropriate to comment further at this time.”