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. (Agencies)
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.
Nadal claimed at the weekend that he found conditions on Chatrier to be different this year after a practice session.
"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.
"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 mediapersons.
A new surface of clay has been laid on the court which should improve day by day, added Tiquet, who said he had some sympathy with the Spaniard.
"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," Tiquet said.
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.
"Also, Monday is club presidents day and most of them will be on Suzanne Lenglen. We want to make sure they have a good day with two French players (Virginie Razzano and Gilles Simon) also scheduled there."
Nadal's fellow professionals admitted they were surprised by the decision to shift Nadal away from Chatrier.
“That's really bizarre," said American 10th seed John Isner.
"I mean, how many times does the guy have to win the tournament to be able to have his first match on Chatrier? I think, no offense to Stan, but, you know, if you look at it, figured they'd be flip? flopped."
The decision caused outrage on social media from fans stunned that the French Open does not follow the same protocol as Wimbledon where the defending champion always opens proceedings on Centre Court.
"This must be a really joke. Nadal on Suzanne Lenglen at his first match of the tournament. 8 time and defending champion," tweeted one fan.
Another wrote: "Don't ever say to me "he's playing
Ginepri bla bla bla... Because Djokovic is playing another joke Joao Sousa and he's on the PC (Chatrier).
Monday's programme got under way over an hour late due to light rain.
Nadal should have few problems against Ginepri who has yet to win a match on the main tour in 2014.
Djokovic defeated 25-year-old Sousa, the world number 44, for the loss of just four games in the third round of the US Open in 2013.
Elsewhere, 2012 women's champion Maria Sharapova opens her campaign first up on Philippe Chatrier against fellow Russian Ksenia Pervak whom she beat at the same stage four years ago.
Third seed and Australian Open champion Wawrinka, who achieved his best result in Paris in 2013 when he made the quarter-finals, has a 4-2 lead in career meetings with Garcia-Lopez.
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.