The fishing industry believes the Emissions Trading Scheme is unfair and serves only what it calls white collar quota owners and not small operators.
A one-off $700,000 unit allocation has been set aside to compensate quota owners for any fall in value of fishing quota resulting from the increase in fuel costs.
Fishing companies Sanford, Aotearoa Fisheries, Sealord and Talley's, who combined, own 80% of the $4 billion quota, stand to benefit most from the emissions scheme.
The Federation of Commercial Fishermen says the Government has taken the easiest road to distributing the credits - not the fairest - which would be to credit all fishing vessel owners.
However, the Government says that would not have been a practical process to undertake.
Applications for ETS credits close at the end of this week.