According to the Rugby Week website, former All Black Schwalger initially suffered the problem last year although it was initially thought to be a chest infection.
Schwalger played just six games for the Hurricanes in 2014 and he also missed Wellington's ITM Cup campaign.
The prop was all set to return this season but last month he got flu which left him bedridden for five days and the clots have returned and he is not allowed any contact until June.
"I was looking forward to jamming with the Hurricanes and playing with Ma'a (Nonu) one last time," Schwalger told the NZ Herald.
Schwalger, 31, spent two years in France but returned to the Hurricanes in 2013 and now comes off contract at the end of the season.
Schwalger said that his goal is to play the final two games of the Super Rugby season in June, although that could extend if the Hurricanes were to make the playoffs.