Guernsey's Sea Fisheries Committee has refused 68 applications from Jersey fishermen to gain access to the island's waters.
Ten other applications have been granted.
Commercial boats have needed a special licence to operate within the 12-mile Bailiwick zone since the start of October.
A commercial boat found operating without such documentation would be liable to a maximum fine of £50,000.
Guernsey had to have a licensing scheme within its 12-mile limit to comply with European regulations.
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They (Jersey) basically wanted to shut up shop and that's come back to haunt them
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But the lack of such a procedure for the Bailiwick area meant any British boat could fish in local waters.
Attempts to reach agreement with Jersey failed, so the Guernsey's Sea Fisheries Committee decided to implement its own scheme.
Sea Fisheries Committee vice-president, Deputy Lyndon Trott, admitted the situation was difficult but claimed the Jersey authorities and fishermen had brought it on themselves.
"The problem is in Jersey where they went for a unilateral system, they did not want to be part of the process," he said.
"They basically wanted to shut up shop and that's come back to haunt them."
The purpose of the licence is to protect fish stocks.
An appeals procedure is in place for the aggrieved parties.