Federer, 36, is taking a break to ensure he is at peak fitness for the defence of his Wimbledon title in June.
Ion Tiriac – the 1970 French Open champion – has accused the Swiss superstar of disrespecting the ATP Tour.
But Becker said: â€śIn principle, Tiriac is right when he says that players are not allowed to chose where to play and where to not.
â€śBut Federer is in another league. He is the best ever. He is an unbelievable tennis player.
â€śHe did all right, and now that he has chosen to skip the clay-court season should be understood.â€ť
Federer is not expected to return to action until the Gerry Weber Open in June as a warm up for Wimbledon.
â€śFederer is in another leagueâ€ť
Tiriac, who hosts the Madrid Open, claimed earlier this month that Federerâ€™s pick-and-mix approach to tournaments would not be welcome in any other elite sports.
The Romanian said: â€śLewis Hamilton does not just say no more after five Grands Prix in Formula One, because he does not feel like it.â€ť
Despite taking a temporary step away from competitive action, Federer is currently involved in a ding-dong battle with Rafael Nadal for the world No 1 ranking.
Nadal snatched top spot back earlier this season and maintained his advantage by winning the Barcelona Open title yesterday.
However, the Spaniard must also reach the Italian Open final next month.
That is because Nadal has plenty of ranking points to defend during the clay court season, while Federer takes another break.