Scotland's environment watchdog has bowed to pressure from the salmon industry to keep secret the number of farmed fish killed by disease, according to internal correspondence seen by the Sunday Herald.

The Scottish Environment Protection Agency (Sepa) agreed to delete information on millions of dead fish from a public database on fish farming launched this month because the Scottish Salmon Producers' Association (SSPO) argued it would be commercially damaging.

Now campaigners against fish farms have accused Sepa of acting like an industry "lapdog". The databaase, which also omits crucial information on sea lice, is no more than "spin", one claimed.

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In February, the Sunday Herald revealed that the number of farmed salmon killed by diseases had leapt to more than 8.5 million in 2012, compared to 6.8 million in 2011 and 5.5 million in 2010. The rise was blamed mostly on the spread of amoebic gill disease.

A few days after the report appeared, SSPO's chairman, Phil Thomas, wrote to Sepa's chief executive, James Curran, accusing it of "fundamentally poor regulatory practice", arguing that it had "no justifiable need" to collect and make available information on the level of fish mortality.

"You were potentially placing information in the public domain which could be used to the commercial detriment or competitive market disadvantage of the companies submitting the data," Thomas wrote. "You were in fact providing competitor companies both within and outwith the UK with significant market and business information."

In reply, Curran said he understood SSPO's concerns, and promised that in future it would be made clear that for most fish farms supplying information on the number of deaths was done voluntarily.

He added: "Although numbers of mortalities do appear in the current version of Scotland's aquaculture database, which is being launched to partner organisations soon, it is our intention to make a small change to ensure that these data on the numbers of mortalities are not included in the version released to the public."

The long-delayed data was published on October 1 by the Scottish Government. Although it includes the weight of fish that have died, it omits the number, which critics say masks the scale of the problem when fish are small.

"Shame on Sepa for morphing into the salmon farming industry's lapdog," said Don Staniford, a veteran campaigner who is now director of a new environmental group, Protect Wild Scotland. "Surely Sepa's statutory duty is to protect the Scottish environment, not cravenly kowtow to the Norwegian-owned salmon farming industry?"

The new database also ignored vital data on the sea lice that often infest caged salmon and threaten wild fish.

Guy Linley-Adams, solicitor to the Salmon and Trout Association (Scotland), argued that the lack of weekly site-specific sea lice data was an "obvious gap" in the database. "It is looking increasingly silly of the Scottish government to refuse to require that data to be published," he said.