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Throughout the European claycourt swing, Dunlop balls were used but the second Grand Slam event of the season has instead opted for Babolat, which generally move faster through the air, as part of a new deal with manufacturers.
"I'm hearing a lot of conversations about the balls. It's just that they're not the same from what we've just played with for the last month," said Federer.
"And that for us is the most frustrating part, that the tournaments all changed to the Roland Garros ball after last year, (but) Roland Garros has changed their balls again.
"Now we're stuck with a different deal for all the different ATP Tour events. That is the frustrating part that we need to adjust before the French."
Britain's Andy Murray said he was unconcerned about the type of ball used but wished it was a consistent choice at the four Grand Slams.
"At the US Open they play with Wilson, and then in the hard court events in the build-up they use Penn. I think just for the players' wrists, joints, like your elbow and shoulder, it makes sense to just stick with the same ball," said Murray.
"The ball probably helps me as it is quite fast. But I would just rather we played with the same ball throughout each part of the season. During the grass, I'd rather all the tournaments were with Slazenger."
The new ball has also caused concern amongst the women players at the French Open, who fear for their physical well-being.
"A lot of the girls are coming in with shoulder issues. They say the balls are pretty hard," said Bethanie Mattek-Sands, the leading US player in Paris.
Novak Djokovic, the world No 2 and one of the favourites to topple Rafael Nadal as French Open champion, believes the big servers could benefit from the changes.
"The balls are very, very fast, so it's really difficult to control. Maybe it's going to favour the servers and the big hitters," said the Serb.
Federer had few problems with either the Babolat ball or first round opponent Feliciano Lopez on Monday as he clinched a 6-3, 6-4, 7-6 (7/3) first-round win, his ninth victory in nine outings against the Spanish left-hander.
The world No 3, playing at his lowest seeding in eight years at a Grand Slam, is taking part in his 46th consecutive Grand Slam tournament.
Federer will next tackle French wild card Maxime Teixeira for a place in the last 32.
Results from the 2011 French Open at Roland Garros on Monday (x denotes seeded player):
Men
First Round
Antonio Veic (CRO) bt Pablo Cuevas (URU) 4-6, 6-3, 6-2, 3-1 - retired
Nikolay Davydenko (RUS x28) bt Denis Gremelmayr (GER) 7-6 (7/2), 6-1, 6-3
Mardy Fish (USA x10) bt Ricardo Mello (BRA) 6-2, 6-7 (11/13), 6-2, 6-4
Marcos Baghdatis (CYP x27) bt Frederico Gil (POR) 7-6 (7/4), 6-2, 6-2
Leonardo Mayer (ARG) bt Dustin Brown (GER) 3-6, 7-6 (7/5), 6-2, 6-2
Albert Ramos (ESP) bt Javier Marti (ESP) 6-3, 6-7 (5/7), 4-6, 6-1, 6-3
Simone Bolelli (ITA) bt Frank Dancevic (CAN) 6-1, 6-3, 6-7 (5/7), 6-2
Tobias Kamke (GER) bt Olivier Rochus (BEL) 6-7 (5/7), 6-3, 6-3, 6-2
Viktor Troicki (SRB x15) bt Julian Reister (GER) 6-4, 6-3, 6-3
Carlos Berlocq (ARG) bt Bernard Tomic (AUS) 7-5, 6-4, 6-2
Alejandro Falla (COL) bt Potito Starace (ITA) 7-6 (7/2), 6-1, 6-1
Steve Darcis (BEL) bt Michael Llodra (FRA x22) 6-7 (5/7), 6-3, 6-3, 6-3
Philipp Petzschner (GER) bt Mischa Zverev (GER) 7-6 (7/3), 6-0, 6-4
Gael Monfils (FRA x9) bt Bjorn Phau (GER) 4-6, 6-3, 7-5, 6-0
Thomas Schoorel (NED) bt Maximo Gonzalez (ARG) 7-6 (7/5), 6-3, 6-3
Igor Andreev (RUS) bt Florent Serra (FRA) 6-4, 6-1, 6-3
Janko Tipsarevic (SRB x29) bt Brian Dabul (ARG) 7-6 (7/1), 6-1, 6-0
Roger Federer (SUI x3) bt Feliciano Lopez (ESP) 6-3, 6-4, 7-6 (7/3)
Stephane Robert (FRA) bt Tomas Berdych (CZE x6) 3-6, 3-6, 6-2, 6-2, 9-7
Marsel Ilhan (TUR) bt Tommy Haas (GER) 6-4, 4-6, 7-6 (7/1), 6-4
Mikhail Kukushkin (KAZ) bt Daniel Brands (GER) 6-2, 6-4, 6-4
Mikhail Youzhny (RUS x12) bt Go Soeda (JPN) 7-5, 6-2, 6-4
Richard Gasquet (FRA x13) bt Radek Stepanek (CZE) 7-5, 6-3, 6-0
Michael Berrer (GER) bt Milos Raonic (CAN x26) 6-4, 4-6, 6-3, 6-4
Marcel Granollers (ESP) bt Alex Bogomolov Jr. (USA) 6-3, 3-6, 7-6 (8/6), 6-2
Thomaz Belluci (BRA x23) bt Andrey Golubev (KAZ) 6-4, 6-4, 6-7 (4/7), 7-6 (7/5)
Juan Martin Del Potro (ARG x25) bt Ivo Karlovic (CRO) 6-7 (7/9), 6-3, 7-5, 6-4
Victor Hanescu (ROM) bt Benoit Paire (FRA) 7-5, 4-6, 6-1, 7-6 (7/4)
Novak Djokovic (SRB x2) bt Thiemo de Bakker (NED) 6-2, 6-1, 6-3
Women
First Round
Caroline Wozniacki (DEN x1) bt Kimiko Date Krumm (JPN) 6-0, 6-2
Aleksandra Wozniak (CAN) bt Junri Namigata (JPN) 6-1, 6-1
Sara Errani (ITA) bt Christina McHale (USA) 6-7 (4/7), 6-2, 9-7
Daniela Hantuchova (SVK x28) bt Zhang Shuai (CHN) 6-3, 6-3
Irina Begu (ROM) bt Aravane Rezai (FRA) 6-3, 6-3
Marion Bartoli (FRA x11) bt Anna Tatishvili (GEO) 1-6, 6-2, 6-1
Olga Govortsova (BLR) bt Agnes Szavay (HUN) 6-4, 4-6, 6-4
Vera Zvonareva (RUS x3) bt Lourdes Domnguez (ESP) 6-3, 6-3
Sabine Lisicki (GER) bt Akgul Amanmuradova (UZB) 6-0, 6-4
Edina Gallovits (ROM) bt Angelique Kerber (GER) 2-6, 6-3, 6-1
Anastasia Rodionova (AUS) bt Nadia Petrova (RUS x26) 6-7 (5/7), 6-3, 6-4
Nuria Llagostera (ESP) bt Anastasia Pivovarova (RUS) 6-3, 6-0
Peng Shuai (CHN x29) bt Tamira Paszek (AUT) 6-3, 6-2
Vesna Dolonts (RUS) bt Anne Keothavong (GBR) 3-6, 7-6 (7/5), 6-4
Francesca Schiavone (ITA x5) bt Melanie Oudin (USA) 6-2, 6-0
Zheng Jie (CHN) bt Sandra Zahlavova (CZE) 6-4, 6-3
Petra Kvitova (CZE x9) bt Greta Arn (HUN) 6-2, 6-1
Kaia Kanepi (EST x16) bt Sofia Arvidsson (SWE) 7-5, 6-1
Heather Watson (GBR) bt Stephanie Foretz (FRA) 7-6 (8/6), 6-1
Roberta Vinci (ITA x30) bt Alberta Brianti (ITA) 6-3, 3-6, 6-3
Iryna Bremond (FRA) bt Evgeniya Rodina (RUS) 6-3, 4-6, 8-6
Jill Craybas (USA) bt Eleni Daniilidou (GRE) 6-3, 6-3
Chan Yung-Jan (TPE) bt Klara Zakopalova (CZE x31) 7-5, 6-1
Sania Mirza (IND) bt Kristina Barrois (GER) 6-3, 6-3
Agnieszka Radwanska (POL x12) bt Patricia Mayr (AUT) 6-1, 6-2
Maria Kirilenko (RUS x25) bt Coco Vandeweghe (USA) 7-6 (7/5), 6-2
Chanelle Scheepers (RSA) bt Viktoriya Kutuzova (UKR) 6-3, 4-6, 6-2
