The club has confirmed on its website that the Japan international has suffered a meniscus ligament tear, and will likely be sidelined for the remainder of the season
The Japan international was injured during the 1-1 draw with AC Milan last weekend, suffering what was initially hoped to be a simple sprain.
However, following further tests carried out by Inter's doctor on Wednesday, the club has confirmed on its official website that the 26-year-old has suffered a tear to his meniscus ligaments and is likely to be sidelined for the remainder of the campaign.
Nagatomo, who joined Andrea Stramaccioni's side from Cesena in 2011, has impressed throughout the current campaign and reportedly attracted the interest of Real Madrid last month.
The player signed a new contract at Guiseppe Meazza at the turn of the year, pledging his future to the club until 2016.