The Pompey boss told how the midfielder was struck down with a bout of food poisoning, leading to him not being able to play in Saturday’s 3-3 draw at Fratton Park.
Thompson was laid low after eating a salmon dish, which led to him being sick during the game after he was named as a substitute.
Managing the 27-year-old’s load of games is also a consideration for Cowley, but the sickness was a major factor in him not getting on the pitch.
Cowley said: ‘I don’t think we’d not want to play Louis.
‘He’s been playing really, really well, the team has been winning consistently and he scored a brilliant goal at Shrewsbury.
‘He actually had sickness during the game.
‘We were hoping we were going to be able to use him.
‘But he was sick during the game, so we couldn’t use him in game
‘These are things you don’t always divulge, but it was just unfortunate.
‘He was feeling unwell and just not in the best condition to come on.’
Pompey have availability concerns going into tonight’s clash with Oxford United at Fratton Park.
But Thompson should be fit for selection after the weekend, as Cowley makes decisions to protect his slimline squad.
He added: ‘We made a decision at 60 minutes at Shrewsbury to keep him on, knowing that would probably mean he couldn’t play on the Saturday.
‘You’ve got someone in really good form and we’re going to have a difficult conversation and leave him out?
‘If anyone thinks as manager we really wanted to do that, they must be crazy.
‘Louis is a really important.
‘Ultimately we have a duty of care for our players and a duty of care for our small squad to make tough but intelligent decisions when necessary.’
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