Civil servants have processed almost 800 applications for the Farm Nutrient Management Scheme this summer.
The Department of Agriculture said the latest tranche of applications was processed after Agriculture Minister Michelle Gildernew announced in June that additional funding had been secured for the scheme.
A second tranche of inspections will begin this week, covering 1,000 FNMS applications received between March 20 and 29, 2006.
Staff are hoping to approve these issued by the end of November before moving on to the third and final tranche.
The department is working towards a deadline of December 31 2008, by which time the EU expects all FNMS works to be completed. The work, required under the Nitrates Directive, is aimed at protecting Ulster's waterways from farm pollution.
Following concerns about the timetable for implementing the FNMS, the Agriculture Minister said in June that further funding had been secured to speed up applications as a result of the decision to sell the AFBI Plant Testing Station at Crossnacreevy.
Applicants whose forms are being processed in the second tranche will receive an early initial contact from a DARD inspector or CAFRE advisor, either to determine a date to complete a pre-approval inspection or to establish what additional information is required, DARD said.
"Farmers who applied during the period from 20-29 March 2006 should ensure that they have, or seek, any necessary approvals from DoE Planning, NIE or the Environment and Heritage Service as soon as possible. These matters continue to be key factors in delaying the approval process," a spokesman said.
"Any FNMS applicant who wishes to withdraw their application can do so. The department asks such applicants to advise their county agricultural office.
"An applicant may reduce the storage capacity for which they applied, providing that the revised capacity meets the minimum requirement. For cattle, that minimum is 22 weeks.
"To meet the EU deadline of December 31, 2008, for getting work done, the department is giving inspection priority over the next seven months to processing approvals.
"As a consequence there may be a delay in inspecting claims for grant payment under the scheme. Farmers are advised to allow for such a delay in making their financial arrangements."