The merger brings together the two largest suppliers of farmed Atlantic salmon in the European area.
This week the UK's Office of Fair Trading (OFT) referred the proposed acquisition to the Competition Commission.
"The OFT has found that the loss of rivalry between these companies may cause an increase in the price of farmed Atlantic salmon, and thereby harm UK consumers," the regulator stated this week. "In addition to this, we found that any effects were likely to be felt more acutely amongst those consumers having a strong preference for Scottish salmon."
The Commission is expected to report by December 20.
Under the UK's Enterprise Act 2002 a relevant merger situation is created if two or more enterprises have ceased to be distinct enterprises; and the value of the turnover in the UK of the enterprise being taken over exceeds £70m.
The merger can also be referred to the Competition Commission if it results in an entity holding a 25 per cent share of a market segment in the UK.
Last month Scotland's Highlands and Islands Enterprise started its own inquiry into the merger, which will result in the combined entity controlling 65 per cent of Scottish farmed salmon production.
The Pan Fish acquisition of Marine Harvest, also involves a merger of Fjord Seafood, all of which will come under the control of John Fredriksen, one of Norway's richest men. The three mergers have already been approved in Norway and in the US.
The agreement would result in the world's biggest farmed salmon producer. The merged entity would control about a fifth of globally farmed salmon, according to estimates.
The Scottish body is concerned about potential job losses in the salmon farming sector.
About 80 per cent to 90 per cent of the output in Scotland is already in the hands of some of the largest companies operating in the region, with smaller players increasingly being squeezed out of the market.
HIE invested about £500,000 in Marine Harvest's processing facility in Fort William three months ago to modernise some of the production lines.
Two salmon processing factories were closed in the Western Isles of Scotland over the past few years. Marine Harvest closed its Stornoway factory in 2003, and then closed a modern factory in Scalpay in 2005, which had received around £7m of public funding.
In March Nutreco entered today into an agreement to sell all of its 75 per cent shareholding in Marine Harvest to the investment fund Geveran Trading for €881m. The agreement would result in the world's biggest farmed salmon producer. The merged entity would control about a fifth of globally farmed salmon.
Geveran Trading is part of Greenwich Holding, a company indirectly controlled by John Fredriksen. Geveran Trading will also acquire the remaining 25 per cent of Marine Harvest, which is held by Stolt-Nielsen.
The Greenwich Group also holds significant stakes in the two Norwegian aquaculture companies Pan Fish and Fjord Seafood.
"The transaction creates fantastic growth opportunities for Marine Harvest," Pan Fish stated in a press release issued then. "As we predicted, the independent joint venture Marine Harvest has indeed acted as a catalyst for further consolidation within the salmon farming industry. It will now be in the centre of a next wave of industry consolidation. This wave will create the sizeable companies in modern aquaculture that will be able to meet the growing demands of consumers all around the globe for high quality and wholesome seafood."
About 60 per cent of Pan Fish Scotland's production goes to customers in the UK. The rest is exported to other EU countries, the US and Japan.
Pan Fish France is based in Finisterre in Brittany and is one of the larger producers of smoked salmon in France. Pan Fish Norway is a fully integrated operation holding 44 licences.