Fishermen in Devon have claimed they are being singled out for increased inspection by the Government.
Fishing industry leaders in Brixham say the Marine Management Organisation (MMO) has become increasingly heavy-handed since new rules were brought in.
One trawler has lost about £15,000 in potential earnings because of the changes and is seeking compensation, its owner said.
The MMO has declined to comment while investigations were ongoing.
It closely monitors catches to protect fish stocks and unveiled a new strategy earlier this year.
Barry Young, from Brixham Trawler Agents, says fishermen have always cooperated with the MMO.
"We're told during a year the MMO is supposed board about 10% of vessels on a quayside," he said.
"But over the last six to eight weeks they have boarded 100% of vessels. Any vessel coming into Brixham has been boarded."
One trawler, the Kerrie Marie, was ordered back to port last month after one of 200 boxes of fish was not recorded in the log.
Its owners said they lost three days fishing and about £15,000 in potential earnings even though no offence was committed. They are now seeking compensation from the MMO.
Owner Dave Langdon said: "We feel like we're being persecuted by the MMO and it's not good. The fisherman is being treated like a common criminal."
However fishermen in Cornwall say they haven't noticed any change.
Elizabeth Stephenson from the Cornish Fish Producers Organisation said: "It's business as usual."
She added: "We haven't noticed any changes, and haven't heard any reports from the boats, out at sea or in the harbour."
The MMO said it has received correspondence in relation to enforcement action at Brixham.
A spokesman said: "The MMO can make no further comment because these matters are still under investigation."