A long-trusted boundary waters partner of the U.S. Forest Service is the subject of a five-year, international criminal investigation into suspected smuggling of Canadian forage fish for commercial resale in northern Minnesota.

According to a document filed in U.S. District Court, three members of a family-operated outfitting business in Ely were watched secretly in the wilderness starting in November 2012. They allegedly netted large quantities of baitfish just inside Canada in apparent violation of the Lacey Act, a century-old anti-trafficking law to protect wildlife.

Investigators watched year after year in late October and early November as the fish were netted during their spawning season directly in front of a Canada Customs cabin, the document said. The cabin normally is unoccupied at that time of year. Some of the netting was filmed by a hidden camera inside the cabin. Agents hiding in the woods also witnessed the activity.

As described in the court document written by Ron Kramer, a Duluth-based U.S. Fish and Wildlife Service agent who heads the investigation, the family members would beach their boat on an island in late afternoon, wade into water and empty their catch into tubs as darkness fell. They returned by boat to their home — a meandering ride of more than 20 minutes across Minnesota’s Sucker, Newfound and Moose lakes.

The site of the activity was Prairie Portage, one of the busiest land crossings into the Boundary Waters Canoe Area (BWCA). The canoe and boat portage at the border of the U.S. and Canada separates Sucker Lake from Basswood Lake, part of which lies in Canada.

At that time of year, with average temperatures in the 20s and 30s, BWCA visitor traffic is next to nil. But throughout canoe season under a Forest Service contract, the family suspected of smuggling the ciscoes charges a fee to paddlers and boaters who want to be pulled over the portage by a truck and trailer.

According to the document, the family members used the portage to enter Canada. When their daily netting was done, they would promptly haul tubs of ciscoes to Ely to be packed and frozen for sale as bait, according to the document. In 2013, the pattern played out on six consecutive days in early November. This year, when snow was on the portage, the harvest was light, according to surveillance described in the court document.

In November 2014, Kramer waited for members of the family to return to Prairie Portage for the cisco spawning season. He wrote the following account:

“I saw them stop in front of the Canadian Customs cabin, then begin a repeated stooping and standing motion which I know from experience to be indicative of fishing using seine nets,’’ Kramer wrote. “The individuals made several trips back and forth between the fishing location in Canada and their boat.’’

The investigation — which became public this month when federal agents raided and searched the outfitter’s business and one Ely bait shop — will be a topic of conversation in northern Minnesota for months, if not years. No charges have been filed, but bait shop owner Jim Maki of Ely criticized the probe this week in media interviews.

“This is a witch hunt,’’ Maki told the Star Tribune.

He said commercial fishing for ciscoes at Prairie Portage has been an Ely tradition for 50 years. He said it’s always done on the U.S. side of the boundary.

Maki said ciscoes — also known as lake herring or tullibees — are prized bait during winter fishing for lake trout and northern pike. Across northern Minnesota, they sell for $5 to nearly $7 a half-dozen. During the harvest season, Maki said, workers at his The Great Outdoors Bait & Tackle store pack and freeze the fish as soon as they are delivered to the door.

In a federal raid of Maki’s shop Dec. 2, law enforcement agents seized “524 half-dozen packages of ciscoes,’’ according to a document signed by Kramer. Agents also confiscated business records and computer data. The probe is proceeding with help from the Minnesota Department of Natural Resources, the Ontario Ministry of Natural Resources, the Royal Canadian Mounted Police, the Duluth Police Department and other agencies.

“I want my fish back,’’ Maki said.

On Dec. 1, also in Ely, federal agents raided the outfitting business operated by the family suspected of smuggling the ciscoes. The court document that authorized the searches said agents extracted data from the mobile phone of one family member and confiscated a binder of business records as well as computer data.

One of the three family members named as a suspect in the document declined to comment. The other two were not contacted. Because the family members have not been charged and have not been outspoken about the case, the Star Tribune isn’t naming them.

The court document said the family has been licensed by Minnesota to commercially harvest ciscoes in Minnesota waters. But Ontario doesn’t allow nonresidents to fish commercially. Sport anglers can legally fish for ciscoes with a dip net in Canada. But the document said the family did not hold a license for dip-netting and used larger seine nets to harvest the fish near a stream that flows from Sucker Lake into Basswood.

Tina Shaw, a law enforcement spokeswoman for U.S. Fish and Wildlife in Bloomington, said Friday the agency’s investigation into the alleged “wildlife crime” will be “ongoing for some time.’’

She declined to comment on the investigation.

Douglas “Gus” Smith, who heads the U.S. Forest Service ranger station in Ely, confirmed that the family suspected of cisco smuggling has long held the contract for motorized portage service at Prairie Portage.

Smith said the family has been a “good cooperator’’ with the Forest Service for many years and that he can’t “hypothesize’’ if the investigation will result in Forest Service sanctions against the family’s business.

“We will take a hard look at it, of course,’’ Smith said.

Smith said his office has taken the position for the past two years that commercial cisco harvesting at Prairie Portage should be banned — even when done with proper state permits. He said the bait trade is an obvious violation of the Wilderness Act of 1964 that bans commercial harvest of fish unless it’s to “enhance recreation in the wilderness.’’

“The Wilderness Act is really clear that we can’t be doing this,’’ Smith said. “It’s not a nuance.’’

For the past two years, Smith said, the Forest Service reluctantly has allowed the Prairie Portage cisco harvest to continue. The forbearance was granted at the repeated request of U.S. Sen. Amy Klobuchar and U.S. Rep. Rick Nolan, Smith said. The requests happened before the smuggling investigation came to light.