The funding will expand the port's facilities, bringing together services and facilities like stores, ice, boxes, water, fuel and repair services into one place.
In addition, the investment is part of an overall £11.4m first round of the European and Maritime Fisheries Fund.
Overall, the funding will be used to expand the floor space of Peterhead's fish market by 50%.
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Speaking on a visit to the port, Mr Ewing said: "This £5 million investment will help cement Peterhead's reputation as not only the biggest European fishing port but the most modern and accessible for fishermen."
Ian Laidlaw, Chief Executive of PPA, added: "Securing Scottish Government and EU (EMFF) support was essential in allowing us to progress with what will be the Port's largest development project in living memory, costing in total £49m.
"Maintaining Peterhead's leading position in the market is not only important for Peterhead and Aberdeenshire but also allows us to continue to make a significant contribution to the Scottish economy. Our investment not only protects existing jobs but also creates employment in the fishing and related industries for the future."
(LM)
