The removal of tonnes of dead fish from a salmon farm before a Scottish parliament fact-finding mission there gave a misleading impression of conditions, an animal rights charity says.

Footage secretly filmed by Animal Equality UK shows salmon being disposed of on Monday morning before a visit to Dunstaffnage salmon farm, near Oban, later that day by committee members carrying out an inquiry into the industry. The committee said the footage raised questions about fish mortality.

Animal Equality UK said tracking data also showed a delousing boat visited the farm three days earlier and dead floating fish were filmed there on the Saturday.

Scottish Sea Farms, which operates the facility and supplies M&S, said removing dead or dying fish was a daily procedure, unconnected to the visit by MSPs. It also denied that the boat referred to by Animal Equality UK was engaged in delousing.

The Holyrood rural affairs and islands (RAI) committee is conducting an inquiry into salmon farming as a follow-up to its 2018 inquiry, which expressed concern about “extremely high mortality rates” at certain sites. It also said the industry had not yet identified an effective way to deal with “the significant challenge presented by sea lice infestation”.

Abigail Penny, executive director of Animal Equality UK, said: “To remove tonnes of dead fish just hours before politicians arrive to investigate is outrageous and depicts a wholly inaccurate image of the industry. We urge the RAI committee to see the industry for what it truly is: deceptive and deadly.

“Given the unnatural conditions, sea lice and diseases run rampant on many Scottish salmon farms. So, while tragic, its unsurprising death rates reached an all-time high over recent years. The 2018 committee already recognised these fatal flaws in the farming system and called for urgent action, but rather than effectively tackle these serious and pervasive issues, this latest move suggests that industry representatives would prefer to hide the truth.”

Data published in July last year by Salmon Scotland showed 56.5% of salmon at Dunstaffnage died during the production cycle. Scottish Sea Farms said that was a result of a micro-jellyfish event and the mortality rate in the current production cycle was 3%.

The RAI committee is scheduled to hear formal evidence from salmon farming representatives on Wednesday next week. Its inquiry is said to be assessing “what progress has been made in developing the industry since 2018 and how the various fish health, environmental and climate change challenges it faces are being addressed”. A spokesperson for the committee said: “We have heard concerns about fish mortality on salmon farms during the wide range of evidence taken throughout our inquiry and this footage raises further questions for the committee.”

Dr Ralph Bickerdike, head of fish health and welfare at Scottish Sea Farms, said: “The footage clearly shows our Dunstaffnage farm team following the company’s standard operating procedure with routine pen-side checks and regular moribund and mortality removal.