Former captain Hughes, who has been playing right-back in this campaign, hurt his groin in the closing stages of Fulham's Barclays Premier League clash against Newcastle and stayed an extra day in London for treatment.
He is expected to arrive in Belfast later on Wednesday but his chances of making the Portugal clash are not thought to be good.
Hibernian defender McGivern, who was expected to replace Lafferty on the left of defence, has a knock and did not train on Wednesday morning.
If Hughes is ruled out it would mean three of the back four from the 1-0 win over Russia - Lafferty and Cathcart the others - are missing on Friday.
The likely return of Manchester United's Jonny Evans alongside Gareth McAuley at centre-half would ease that blow somewhat, but improvisations may need to be made elsewhere.
Uncapped Kilmarnock left-back Rory McKeown is one alternative, as is Hull's Alex Bruce - who can play across the back four - while Shane Ferguson could be asked to move back from his usual midfield position.
O'Neill is also understood to be pondering a call-up for Chris Baird, an experienced international who has been left out having failed to agree a deal since his release by Fulham at the end of last season.