The versatile defender is being assessed for a similar problem which he struggled with before arriving from Swindon Town.
The 26-year-old has yet to feature for Pompey after becoming Kenny Jackett’s first signing a manager.
He missed the opening friendly with Salisbury before being ruled out of Saturday’s trip to the Hawks.
Jackett admitted the situation with Thompson is a blow.
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The Blues boss said: ‘Nathan Thompson is having a scan but it looks like he’s got a problem with the bottom of his foot.
‘It’s the other side (to a similar problem he had last season) but he has a problem with the base and sole of his foot.
‘It’s kept him out and is being diagnosed now but it’s slightly frustrating.’