A former head of BC Hydro has been charged with violating the Fisheries Act by allegedly damaging local salmon habitat at his waterfront property in West Vancouver, CBC News has learned.

John Laxton, a Chair of BC Hydro in the mid 1990s, has built a massive breakwater in front of four waterfront properties he owns, but fisheries officials allege the structure could affect wild salmon stocks.

In an information to obtain a search warrant obtained by CBC News, the DFO lays out its case, claiming Laxton wanted to rebuild the breakwater after it was damaged by a storm.

But starting in January 2011, fisheries officers warned Laxton that the work was endangering local fish, the documents say.

The documents also say that during repeated surprise inspections, the DFO found heavy equipment digging on or near the shoreline with plumes of sediment running into the ocean and a large hose pumping turbid water into Howe Sound.

In March 2011, DFO issued an "inspector's directive," in effect, a cease and desist order.

In April, Laxton responded, "We believe we have a right to place rock on the property we own … We do not believe you have the jurisdiction.”

Laxton faces nine counts under the Fisheries Act, including harmful alteration of a fish habitat, delivering a deleterious substance and failing to comply with the direction of an inspector.

John Laxton appears before the media during the so-called Hydrogate affair. (CBC)

A neighbour of Laxton and the construction company that did the work are also facing charges.

Laxton is no stranger to controversy. He was forced to resign from BC Hydro over the "Hydrogate affair," in which he was found to have invested in a power project in Pakistan in which BC Hydro was also involved.

Laxton and his co-accused are scheduled to be in North Vancouver court in August to face the current charges.

The charges over the breakwater have yet to be proven, but a conviction could carry fines of up $300,000.

In a statement sent to CBC News late Thursday, Laxton spokeswoman Natalie Cade said the repair work [on the breakwater], "was carried out on the advice of reputable experts in fish habitat who have been able to confirm that the repair work has been well done and has considerably improved the fish habitat."

Cade said Laxton is in the midst of a bureaucratic squabble within the federal government.

"Unfortunately Mr. Laxton has found himself caught in the cross-fire between the D.F.O. and the Government who are making major amendments to the Fisheries Act to repeal the sections under which the D.F.O. is attempting to proceed," Cade said.

With files from the CBC's Eric Rankin