Nadal, who has a phenomenal record of eight titles, 59 match wins and just one loss in Paris, had his opening match against US wildcard Robby Ginepri, the world number 279, shifted out to Suzanne Lenglen court.
However, Roland Garros's showpiece Philippe Chatrier court will stage title rival Novak Djokovic's match against Joao Sousa and Stan Wawrinka's clash against Guillermo Garcia-Lopez.
The main court will also host opening women's matches featuring Maria Sharapova and home player Alize Cornet.
"I think they made the court new, so it's like the clay gets a little bit more fixed. It was moving around a little bit too much and some small stones make the movement a little bit more difficult," said Nadal.
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"But probably they will be ready for the tournament now. They can fix it. They are specialists, no?"
However, his complaints stunned ground staff at Roland Garros.
"I was surprised because nobody else had complained about Chatrier," Gerard Tiquet, the man in charge of the courts for 22 years, told L'Equipe newspaper.
"I understand his fears. Nadal needs to anchor his feet on the clay. I also believe he is worried about a repeat of the problems he had with the blue clay in Madrid in 2012. The clay there was slippy and grainy."
- Balance courts -
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Remy Azemar, the assistant referee, insisted that schedulers had to balance the needs of the players as well as the fans.
"There was a discussion. We wanted to have a balance with Nadal on one court and Djokovic on the other," he said.