Foraging trip duration of breeding seabirds is affected by characteristics of available feeding habitat in the marine environment, which may, in turn, generate inter-colony difference in the patterns of nest attendance. Here, nest attendance patterns and foraging areas of Streaked Shearwaters (Calonectris leucomelas) during their incubation period were examined using global location sensors. The study was conducted at Sangan (SI) and Mikura Islands (MI) in the northwestern Pacific, and Awa Island (AI) in the Japan Sea during 2006–2009. The duration of incubation shifts showed significant inter-colony difference, but no sex-related difference. Shearwaters from SI had shorter mean incubation shifts (5.6 days on average; range 3.0-8.0 days) than those from MI (7.2 days; range 4.8–10.7 days) and AI (6.9 days; range 6.0–9.7 days). During the incubation period, SI and MI shearwaters foraged in the northwestern Pacific's Kuroshio-Oyashio transition area, while shearwaters from AI mostly foraged in the Japan Sea. The Northwestern Pacific represents a high-productivity zone, and SI shearwaters appeared to forage in these waters, where foraging efficiency is potentially high, leading to shorter incubation shifts. Also, although MI shearwaters foraged in the northwestern Pacific, the distance between their colony and foraging areas was greater (645 km on average; range 546–756 km), compared to SI (272 km; range 244–297 km) and AI birds (228 km; range 75–518 km). In this study, inter-colony differences in incubation shift length of Streaked Shearwaters appeared to be related to differences in foraging areas associated with the local marine environment.