"He couldn't run and couldn't work in the pool with it, so I don't know what the prognosis is," said Saints coach Wayne Smith.
Thompson now has a week of intensive therapy ahead of him if he is to feature in the RBS 6 Nations opener against Italy.
The good news for Sir Clive Woodward from Franklin's Gardens was the form of scrum-half Matt Dawson and wing Ben Cohen.
Dawson made only his second Premiership start of the season after shrugging off shoulder and calf injuries and set up Oriol Ripol's first-half try with a trademark darting break.
Cohen was dangerous all afternoon, finally scoring after a powerful hand-off left Anthony Elliott flat on his back.
And Northampton coach Smith was delighted with a hard-earned win that made up for the disappointment the previous weekend's European Cup exit.
"It's been a difficult week which is a hangover from not making the quarter-finals of the European Cup," said Smith.
"We had to pick them up and go out with an approach that was positive and looking forward.
"We've tried to re-energise this week but subconsciously there was a lot of disappointment and that manifested itself in a sluggish performance today.
"Rotherham played with real passion and you've got to take your hats off to them. I'm just grateful we got the four points."
The Yorkshire side are still searching for a first Premiership win of the season after 15 defeats but were on top for long spells and had a crucial try disallowed at the death.
"The players and coaching staff can take a lot of heart from the performance," said coach Steph Nel. "We're getting there slowly and surely."