Robert Gillam and the groups are accused of breaking the law during last year's ballot measure campaign to block the mine.
Gillam is president and chief investment officer of Anchorage-based McKinley Capital Management, an investment firm managing more than $4 billion for individuals and institutions. He also is an avid fisherman who owns a large home on Lake Clark near the Pebble prospect. He has helped bankroll the opponents' campaign.
The proposed mine is controversial due to its location in the headwaters of two of the five rivers that feed Bristol Bay's world-class salmon runs.
In late March, the two companies trying to develop the copper and gold mine and the Resource Development Council, an Anchorage business group, filed a complaint with election regulators. They are accusing Gillam and the advocacy groups of illegally hiding nearly $2 million of donations from Gillam to the anti-Pebble campaign.
The crux of Pebble's accusations is that Gillam secretly gave nearly $2 million to the Anchorage-based Renewable Resources Coalition and the Virginia-based Americans for Job Security, which then funneled the money to a pro-Measure 4 ballot group, Alaskans for Clean Water, to help pay for the campaign.
The donations to the groups were an illegal "pass through," according to Pebble. They based their 16-page accusation on e-mail exchanges between Gillam and the groups before, during and after the ballot measure campaign.
The ballot measure, rejected by voters in August, was an attempt by Pebble opponents to require stricter limits on water-pollution discharges from large mines.
Gillam and the groups say in legal documents that the money he provided to them during last year's fight over Ballot Measure 4, the "Clean Water" initiative, did not break any laws.
Most of the allegations lack legal foundation, deliberately misrepresent facts or lack evidence to back them up, the groups said in their filing to the Alaska Public Offices Commission.
"The fact that Pebble has nonetheless filed such allegations ... is a reflection of its true motive to smear (its opponents)," a filing said.
Pebble opponents have been waging a high-profile advertising and lobbying campaign against the proposed mine in Southwest Alaska for several years.