The Netherlands was a 4-3 winner over Austria in its only match in the last month but a devaluation of points from matches in previous years saw it lose 172 points in the rankings.
That allowed Germany, which gained 13 points, and Uruguay, which is up 20 points, to pass the Netherlands.
Spain also saw a significant adjustment in points, going from 1,561 in March to 1,442 this month. But the Spaniards are still No. 1 with 97 more points than Germany (1,345) while Uruguay is third with 1,309 and the Netherlands totals 1,207.
The No. 3 ranking is an all-time best for Uruguay.
Spain was the only team in the Top 10 not to change its position this month.
Portugal (1,190) is up two places to No. 5, pushing Brazil (1,165) and England (1,132) both down one spot to sixth and seventh, respectively.
Croatia (1,114) and Denmark (1,069) are both up two to eighth and ninth while Argentina (1,066) drops from No. 8 to 10th.
Italy was ninth last month but drops out of the Top 10 to 12th in April.
The FIFA world rankings are determined by points awarded from match results in a three-year period, with more recent games given greater weight. Teams get additional points for playing relatively strong opponents. The next FIFA men's rankings are to be released May 9.
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