In 2008 and 2009 seasons, a sudden increase in Potato virus Y (PVY) incidence was recorded in foundation seed potatoes in Hokkaido, northern Japan. This increase was obvious during the field inspection and the postharvest indexing. Molecular typing revealed that besides the previously reported strains of PVYO and PVYNA-N, the most common strain identified was the recombinant PVYNTN, with three characteristic recombinant junctions at the HC-Pro, VPg and CP regions. No potato tuber necrotic ringspot disease (PTNRD) was observed in foundation seed potatoes in correlation with the presence of PVYNTN. Moreover, an isolate with a typical PVYNTN recombinant genome, namely Eu-12Jp, did not induce PTNRD in 62 Japanese potato cultivars tested in both primarily and secondarily infected plants. Two cultivars carrying the extreme resistance gene Rychc were resistant to the infection with Eu-12Jp, which presents potential sources of resistance to PVYNTN. Eu-12Jp induced systemic mottle in potato cultivars Desiree and King Edward carrying resistance genes Ny and Nc, respectively, but induced a hypersensitive reaction in potato cultivar Maris Bard, with the Nz hypothetical resistance gene typical of the PVYZ strain group. Therefore, based on the genome structure and the reaction of the potato N resistance genes, Eu-12Jp should be classified as PVYZ-NTN, as described for isolates from Idaho, USA recently. This is the first report of PVYZ-NTN in Japan and the sudden and increased occurrence of PVYNTN/PVYZ-NTN represents a potential risk of PTNRD developing and increases the significance of PVY in Japan.