"Under doctor's advice I have had to withdraw from the Godo tournament due to my elbow injury. I'm going to take four or five days of rest," said the Scot, who had tested his problem without much success on a side court at the Real Club de Tenis hours earlier.
Witnesses said the player's fitness looked questionable as he tried to serve, 72 hours after he had to take a pain-killing cortisone injection in order to play a Monte Carlo Masters semi-final against Rafael Nadal.
Murray will hope to be fit for the Madrid and Rome Masters events, which precede the May 22 start of the French Open.
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On the court, French ninth seed Richard Gasquet booked into the second round with a 2-6 7-6 (7-2) 6-4 defeat of Juan Ignacio Chela.
Gasquet, a third-round victim last week in Monte Carlo against Nadal, fought for more than two and a half hours to put out his Argentine opponent, overcoming six potentially costly double-faults against Chela.
World number 17 Gasquet faced 11 break points, saving six, while breaking clay-court specialist Chela four times.
He will next play Slovenian Blaze Kavcic.
Former US Open winner Juan Carlos Ferrero, 2001 champion in Barcelona, made a winning return in his first match since New York last autumn after undergoing surgery on his wrist and knee in October.
The veteran Spaniard reached the second round by beating Belgian Xavier Malisse 6-4 6-2.
He now has a 26-9 win-loss record in Barcelona, where he has played finals in 2000 (lost to Marat Safin) and 2005 (lost to Nadal).
"I had some discomfort at first, but after I warmed up I felt better," said Ferrero. "It did hurt everywhere at the end and it was hard to close out the win. But I'm happy, everything went well."
Japan's Kei Nishikori advanced when Spain's Per Riba retired injured at 6-2 down after the first set.
The same fate befell this month's Casablanca champion Potito Starace of Italy, who could not go on against Spaniard Daniel Gimeno-Traver with the score 4-6 6-1 2-0 in Gimeno-Traver's favour.
Gimeno-Traver will next face five-time champion Nadal, fresh from a seventh consecutive title at Monte Carlo, where he defeated Barcelona fourth seed David Ferrer.
In other results, Croatian Ivan Dodig defeated Frenchman Vincent Millot 6-2 6-3, while the last remaining German, Simon Greul, eliminated the only American in the singles field with a 6-4 6-4 defeat of Robert Kendrick.
