The short answer is that lower leverage is offered on pairs having higher perceived risk for volatility, potentially resulting in disorderly markets. This is a judgement call on the part of individual brokers.
As for special circumstances currently affecting the yen pairs, you might want to refer to this LINK.
Maximum allowable leverage – and therefore required initial margin – are the same on yen pairs (except for AUD/JPY) at the two largest U.S. retail brokers, Oanda and Forex•com.
At both of those brokers, required margins are 4% (corresponding to 25:1 max. leverage) on CAD/JPY, CHF/JPY, EUR/JPY, NZD/JPY, and USD/JPY; and 5% (corresponding to 20:1 max. leverage) on GBP/JPY.
Oanda requires 4% margin on AUD/JPY, as well.
Forex•com, by comparison, requires 3% margin (corresponding to 33.3:1 max leverage) on AUD/JPY.
You can compare all the pairs offered by these two brokers at –