With the World Cup in England a little over four months away, the Springboks suddenly have problems in a position where they have enjoyed so much depth down the years.
The latest setback was confirmed on Monday when Meyer told reporters that lock Flip van der Merwe, a certainty for his World Cup squad if fit, had made himself unavailable for international rugby this year for undisclosed reasons.
"Flip is not available for international rugby at the moment," Meyer told reporters.
"It is a big setback as I've always rated him and he is an enforcer. You need an enforcer for international rugby and he can play at (number) five as well.
"He would be in this squad but unfortunately he isn't available."
The retirement of veteran Bakkies Botha, Andries Bekker's move to Japan two years ago and injuries to current campaigners has left Meyer sweating over his options in the second row.
"Eben (Etzebeth) is recovering from injury, Pieter-Steph (du Toit) is injured and Victor (Matfield) has been out with a knee (injury), so if there is one position I'm worried about, that is it," he said.
"There are one or two loose forwards that can play lock but you need specialists there. Lood (de Jager) is also injured, so if I had to pick a side today we'd be in trouble with locks."
Meyer admitted his other area of concern was at centre, with captain Jean de Villiers progressing well in his recovery from a major knee injury but still touch-and-go for the World Cup.
"Flyhalves we are doing fine and there enough nines (scrumhalf), but the other position I'm worried about is centre. We have had a lot of injuries in the midfield, while at fullback there are players coming through."
The World Cup takes place from Sept. 18 to Oct. 31, where South Africa have been drawn in Pool B, alongside Japan, Samoa, Scotland and the United States.
(Reporting by Nick Said; Editing by John O'Brien)
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