At the end of 5 years, however, the agency will be able to report the expenses to be categorized as research and development rather than the outlays for each of the preceding 5 years.
The agency can categorize the expenses as cost of goods sold rather than research and development. 
mnli hypothesis: The agency can categorize the expenses as cost of goods sold rather than research and development.  premise: At the end of 5 years, however, the agency will be able to report the expenses to be categorized as research and development rather than the outlays for each of the preceding 5 years.