Cardiff City are suffering even more injury woe after their 1-1 draw with Blackpool as their injury worries mount.
Young striker Josh Magennis, who made his first Championship start, was stretchered off in the first half with a broken leg.
And winger Chris Burke was forced off with a rib injury, while others played despite suffering from a virus.
“We will have a head count and see how everybody is,” said Jones ahead of tonight’s third round clash at Bristol City.
“I’ve got three or four lads in there throwing up who could have easily come off, but the likes of Kevin McNaughton stayed on. Ross McCormack couldn't as he’s not too good.
“We’ve got Burkey with a rib injury, Josh who’s picked up a broken leg and Jay (Bothroyd) down with illness.
“Also we’ve got Joe (Ledley) carrying on with his hip injury, and Gavin (Rae) since he broke his hand, he's only had two days training.”
Nigel Clough must pick his Derby County side up from their 4-1 drubbing at home to Scunthorpe on Saturday as Millwall visit Pride Park this evening.
Clough, who saw his team extend their winless run to five games against Nigel Adkins men, believes the squad are suffering from a severe loss of confidence.
“This is as low as we have been for a long time,” he admitted. “We just don't seem to have the character out there at the moment to get back in the game.
"Whether it is too much for some of them I am not sure.”
Portsmouth must do without Jamie O'Hara for their third-round clash at Coventry under the terms of his loan deal with Spurs.
But England goalkeeper David James could return from a calf problem, and Aaron Mokoena is available again after suspension.
Nadir Belhadj, Hassan Yebda, Aruna Dindane and Kanu are representing their countries in the African Nations Cup.
Nottingham Forest’s and Birmingham City’s unbeaten runs will be tested once again as the duo meet at St Andrews in their third round replay following a 0-0 stalemate in their first meeting.
Sheffield United and QPR will meet at Loftus Road in their third round replay, although Accrington Stanley’s tie against Gillingham and Doncaster v Brentford were both frozen off.
Notts County bid to entertain Forest Green for the first time has again been frozen off, although the game has been rescheduled for next Tuesday.
League One title challengers Norwich’s attempt to close the gap on leaders Leeds to three points with a win at Walsall have been denied by a frozen Bescot Stadium pitch.
The League Two matches between Aldershot and visiting Bradford, and Bury’s game with Macclesfield have both fallen foul of the weather.