Commenting on the flanker's chances of playing, Brian McLaughlin said: "Stephen is progressing, we are assessing him on a daily basis and we will see how he gets on.
"The scan he had has sorted out a few issues for the medics. It's a battle against time but we have our fingers crossed.
"He's doubtful but we still have hope that he will be fit. We will leave it with the medics and make the decision as late as possible."
Mike McComish has returned to full training and has been named in the extended squad for the first time since suffering concussion during the Edinburgh match over a month ago.
Second row Tim Barker (back) and winger Simon Danielli (hamstring) remain sidelined, while young backs James McKinney (shoulder) and Chris Coachrane (foot) have also picked up injuries.
Munster's 18-9 derby defeat to Leinster last Saturday was their first home defeat in a competitive game this season.
They have injury concerns of their own, but captain Paul O'Connell, Conor Murray, Donnacha Ryan and Keith Earls are all expected to play.
The Munstermen progressed unbeaten through their pool, a great achievement given that their opponents were last year's beaten finalists Northampton, the Scarlets and Castres Olympique.
Ulster go into Sunday's fixture in good form themselves, having won their last three games in the RaboDirect PRO12 and scored 15 tries in the process.
Looking forward to the last-eight date in Limerick, winger Andrew Trimble said: "We are getting excited about the quarter-final. It's great to be still involved in two competitions at this stage of the season.
"We know the significance of the game. We need to be on top of our game and produce a massive performance if we are to get a result either way.
"It makes the business end of the season so much more exciting (when you're challenging for trophies). There’s nothing worse than looking forward to a Connacht game (at the end of the season) and the winner qualifies for the Heineken Cup the following season.
"It's just miserable. We want to be winning trophies. There is going to be a lot of intensity in the games over the next few weeks but I think we can cope with that."
ULSTER Squad (v Munster) - Backs (14): Paul Marshall, Ruan Pienaar, Ian Porter, Ian Humphreys, Paddy Jackson, Luke Marshall, Paddy Wallace, Ian Whitten, Nevin Spence, Darren Cave, Stefan Terblanche, Conor Gaston, Craig Gilroy, Andrew Trimble, Adam D'Arcy.
Forwards (19): Callum Black, Tom Court, Adam Macklin, Declan Fitzpatrick, John Afoa, Paddy McAllister, Rory Best, Nigel Brady, Andi Kyriacou, Lewis Stevenson, Dan Tuohy, Johann Muller (capt), Neil McComb, Stephen Ferris, Mike McComish, Willie Faloon, Pedrie Wannenburg, Chris Henry, Robbie Diack.