The Spaniard, who has in the past called the calendar "crazy" and "overloaded", was disappointed not to play on home soil but after enduring a year of injuries, he felt he had no choice but to take a break to preserve his body for the French Open.
"I have said on repeated occasions that the tennis calendar, especially this part of the claycourt season, is poorly thought out and not playing in Barcelona, I feel, is a consequence of this," the former world number one said in a statement posted on the tournament website.
"It's very tough not to play in Barcelona, more than any other tournament. But this year after the victory in Monte Carlo my body has called for me to rest. It is particularly painful... because I regard this as my home competition," he added.
Nadal was in breathtaking form as he dismissed Davis Cup team mate Fernando Verdasco 6-0, 6-1 in the final of the Monte Carlo Open on Sunday, but the effort looks to have taken a heavy toll on his troublesome knees.
In the past, the world number three has often pushed his body to the limit by playing on the energy sapping clay for three or four weeks in a row. But after being forced to miss the entire grasscourt season in 2009 to nurse his stricken knees, Nadal has opted to take a more cautious approach.
In the run up to Roland Garros, which begins on May 23, he is expected to play in Masters events in Rome and Madrid.
Tournament director Albert Costa said: "We wish Rafa the best of luck. We know it is a measured decision and that it will have been tough to take. The player has to know when to listen to his body."
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