Niall Ronan was carried off three minutes from half-time as his latest comeback from injury ended in more despair.
And there was a further setback for Munster as they fell to their third defeat of the season and their first in 16 games to Scarlets.
Ronan was on the receiving end of a hefty blow to the head at Musgrave Park after he collided at ruck time with Scarlets lock Jake Ball, but, despite receiving treatment on the field for seven minutes, initial reports suggest that his injury was not as serious as first feared.
"It looked like a relatively serious neck injury, but we've got information coming in that it's not significant and we'll just have to wait and see and hope for positive news over the next wee while," said Munster coach Rob Penney, who saw his side taste their first defeat in Musgrave Park since 2008.
"He's had a rash of injuries over his career and it would be great to see him get a solid run."
Simon Easterby's Scarlets continue their charge thanks to Andy Fenby's try late in desperate conditions at the Cork venue, but JJ Hanrahan snatched a deserved losing bonus point for the home side with a late penalty.
Penney felt his side didn't cope well in the squalid conditions.
"In those conditions when the opportunities arise you've really got to be able to take them and we probably had two clear try-scoring opportunities in the first half that we didn't nail.
"We got a bit frustrated at scrum time and we lost our way a little bit there and that really cost us too today," Penney said.
After the sides shared six points in the opening half, the game was in the balance midway through the second half, with Munster camped deep in Scarlets' territory.
However, a set move off the back of a scrum failed when Luke O'Dea fumbled in the horrible conditions.
And, within seconds, Munster had conceded the crucial try. Felix Jones had two chances to gather and clear the danger inside his own '22,' but he also couldn't gather the ball and Fenby dived on the spillage and got the vital downward pressure.
The excellent Aled Thomas landed the difficult conversion to clinch the victory, and Munster needed Hanrahan's late kick into the teeth of the Musgrave gale to pick up anything for their efforts.
Ronan's misfortune meant an earlier than expected introduction for new South African back-row CJ Stander and on the verge of half-time he came within inches of making an instant impact, only for the television match official to rule that he had been held short of the line.
Ian Keatley had earlier kicked Munster into a 3-0 lead in the 23rd minute after a sustained period of pressure from Penney's side.
After the sides went in 3-3 at the break, Munster faced the worst of the conditions on the turnaround and in his first competitive Pro12 game, referee Laurent Cardona was handed a tough introduction to the league.
He awarded Scarlets another penalty, which stemmed from a wheeled scrum and which Thomas converted in the 67th minute.
Three minutes later the Welsh side sealed the win with Fenby's sixth try of the season.
Munster – F Jones; D Howlett, C Laulala, J Downey, L O'Dea (D Hurley 71); I Keatley (JJ Hanrahan 71), D Williams (P Stringer 72); W du Preez (M Horan 68), M Sherry (D Varley 68), S Archer ( BJ Botha 44); I Nagle (D Foley 71), B Holland; Dave O'Callaghan, N Ronan (CJ Stander 36), P Butler.
Scarlets – M Stoddart (D Newton 58); N Reynolds, G Maule, G Owen (A Warren 74), A Fenby; A Thomas, G Davies (R Williams 74); P John (S Hopkins 75), E Phillips (K Myhill 74), J Adriaanse (S Lee 53); J Ball, R Kelly; G Earle (J Snyman 63), J Edwards (D Thomas 44), C Price.
Ref – Laurent Cardona (FFR)