The harbor of Hakodate Port, which had been shallow since long before, had deposition of sediments so that it became impossible for large vessels to reach the shore; in 1892, in response to the submission of "Proposal for dredging and repairs of Hakodate Harbor and construction of a dock," a request for repairs of Hakodate Harbor, Kitagaki directed dredging work of the harbor and construction of sand control dyke, breakwater and lighthouse as well as improvement works including construction of a wharf by reclaiming land from the sea.
1892年（明治25年）、もともと港湾部が浅かった上に土砂の堆積が重なって大型船の接岸が不可能になっていた函館港の改修についての要望書『函館港湾浚渫修築并ニ船渠設置意見上申書』の提出を受け、港内の浚渫や砂防堤・防波堤・灯台の設置、埋立てによる埠頭の建設などの改良工事を指示した。