Adding to the woe are injuries to key playmaker Rhys Priestland and flanker Dan Lydiate with knee and ankle injuries respectively. Both are rated as 50/50 chances for making the Irish encounter.
"Gethin is struggling and could be out for four to five weeks. Rhys will be struggling for the first game. We're assessing him day by day," said Gatland.
He added: "Dan Lydiate is touch and go. We're hoping Jamie Roberts will be OK".
Gatland admitted the loss of Lions front row Jenkins and Priestland, will be tough acts to follow.
"Gethin is a huge loss for us for potentially the first two games of the tournament. He's been playing exceptionally well for the Blues in the last month.
"He's a world class player. He's got a very good rugby brain and is able to asses things on the field. He's almost like a coach on the field.
"You get a lot of information from him at half-time, what's going right or wrong, tactically where we need to change.
"Rhys was probably the find, if not the best, fly-half at the World Cup. He really does fit the type of game we want to play. His kicking game and vision are excellent. He stretches opposition defences as well because he's not afraid to run.
"There's a very good balance to his game. You can't underestimate the space he created for our midfield at the World Cup.
"He was one of the reasons we saw some really big performances from Jamie Roberts, Jon Davies and Scott Williams. He will be a big loss for us.
"But there's experience to come in with James Hook and we may look at Gavin Henson in that position too."