Is it plagiarism to publish work that is contained in a final report to the funder?
If the final report to the funder is kept confidential by the sponsor and not used for external purposes, then turning that report into a publication is not really self-plagiarism. It's similar to the logic that the contents of NSF and NIH proposals are not publications, and therefore material from them can be recycled later into publications.

In the present case, where the report is "published," you need to check with the journal to which you would like to submit your manuscript and determine what the journal's "prior use" policies are. Not all journals operate under the same set of rules. 

My answer to the question Is there a downside to “publishing” a preprint first? and the comments are worth reading.