Benitez feared the worst last night and x-rays at the club's Melwood training ground today have confirmed he has fractured a metatarsal in his right foot.
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"He's had x-rays today and they confirmed he has a broken metatarsal.
"We have to check over the next couple of days how long it will take to recover."
Skrtel's absence, however long or short it turns out to be, comes just as Benitez thought he finally had a full-strength squad with which to tackle their remaining 11 matches as they bid to secure Champions League football next season.
Striker Fernando Torres and midfielder Yossi Benayoun, both so important to Liverpool's attacking options, have both returned in the last week after more than a month on the sidelines with injury.
Even £17 million summer signing Glen Johnson is nearing a comeback, having not played since late December because of a knee injury.
"He's doing well. He was training today with the team - a light training session," said Benitez.
"I was watching him and he was quite sharp but Sunday will be too soon."
Jamie Carragher has been filling the England international's spot on the right of defence in the interim but with Skrtel now ruled out of Sunday's Barclays Premier League clash at home to Blackburn and Sotirios Kyrgiakos suspended, Liverpool's vice-captain is likely to switch back to the centre.
That leaves an opening which could be filled by Philipp Degen, Martin Kelly or Stephen Darby.