The Swiss superstar was slammed Julien Benneteau last month for how much influence he wields in the game.
Benneteau claimed Federer put his involvement in the Laver Cup over the Davis Cup.
He then accused the International Tennis Federation of being “weak” in their handling of the two events.
The 36-year-old also highlighted a conflict of interest in Australian Open tournament director Craig Tiley being involved in the Laver Cup and deciding Federer’s match schedule.
Krajicek has hailed Federer but claimed issues could arise if Rafael Nadal and Novak Djokovic start flexing their muscles too.
“I understand Benneteau’s point of view but Federer is just amazing” he told Nos.
“No one gets attention the way he does so it’s not surprising that Federer often plays at night.
“It will become a problem only if opponents Nadal and Djokovic will complain about it, so you have to get worried as a Tournament.
“But I don’t remember someone criticised Federer’s schedule.
“It was always said that the Rome clay-courts tournament wanted Becker to win so the tournament had made the balls tougher and had put less clay on court.”
Despite Krajicek’s warm words, the Dutchman has previously claimed Federer – and Nadal – only have a few more years left at the top.
“I have been saying for more or less a year that their last year is closer,” he said.
“Now I feel that both of them will last for two more years.
“I am sure that they will be able to win a Grand Slam tournament on their favourite surface.
“So Nadal can still win on clay at the French Open and Federer on grass at Wimbledon.
“Federer could look at 2020 Olympics in Tokyo as a moment to say goodbye. He loves the game so much that he wants to continue.”
Krajicek also lauded Djokovic for his Grand Slam triumphs in 2018.
“Novak Djokovic’s comeback as the dominator of men’s tennis,” he said when asked about the sport’s biggest moment.
“The Wimbledon semi-final between Djokovic and Rafael Nadal says it all. It included everything.
“The level was ridiculous, the show went on for two days.
“Djokovic was almost untouchable in the second half of the year but not so good as in the first time of his dominance.
“Otherwise, he would have won the ATP Finals.
“I have to mention also Roger Federer, who won his 20th Grand Slam title in January and who became the world number one again in February after five years.
“His first title came in Melbourne, the second one at the ABN Amro tournament in Rotterdam and it was special for me.”