Under the new shōgun Tokugawa Iesada, and with the situation in Ezo in light of Russian activity increasingly a priority, the significance of his endeavours began to receive recognition from the top: in 1855 he was given ten ryō of gold by the bakufu, with twice as much arriving in the next few days from Tokugawa Nariaki, daimyō of Mito Domain, and Date Yoshikuni, daimyō of Sendai Domain. He received instructions to travel to Ezo again, this time as an employee of the bakufu, for further work on its geography, to investigate its mountains and rivers, and the potential for new roads. Over the next three years, three visits would ensue—indeed, one theory sees those earlier not as private initiatives, but operations in the pay of the bakufu, connecting this to the obstacles placed in his way by the Matsumae Domain. Joining the expedition headed by , he completed a circuit of the island, travelling clockwise from Hakodate, also crossing the Sōya Strait to the northern regions of Ezo, as far as what is now Poronaysk, on Sakhalin. Mukōyama died along the way, Matsuura himself so ill that he composed a death poem. The following year, abandoning plans for further investigation of Sakhalin, he followed the courses of the Ishikari and Teshio Rivers, from their mouths to their upstream regions. His final visit, in 1858, included investigation of the interior of the centre and the east of the island, around Akan. His surveys covered both physical and human geography, and suggestions for the development of the land and the advancement of its inhabitants. Records of these three years run to 117 volumes, while he also aimed at a wider audience through works such as Ezo Manga and a series of travelogues full of detail on the local mountains and rivers, flaura and fauna, and the customs, legends, and material culture of the Ainu he encountered along the way. Sympathetic to their plight, his 1858 , which includes their sufferings at the hands of traders and officials of the Matsumae Domain, was refused for publication by the Hakodate bugyō.
