The Aussie fell 0.7 percent on the day to 93.77 yen, from a four-year peak of 94.63 yen.
The kiwi was harder hit, slipping 0.9 percent to 74.70 yen after it had scored a fresh peak of 75.49 yen earlier in the session, its highest since Sept 2008.
"The Aussie went from 79 to 95 yen (in three months), so around 20 percent... That is quite a dramatic move. Having the currency gone so far already, left it vulnerable to a pullback," said Matthew Johnson, a rate strategist at UBS.
He said the Japanese government would probably still favour more yen weakness and does not expect a major correction.
"(But) It's certainly a reminder to people that it's not a one-way bet," Johnson added.
The yen leapt across the board after Amari said an excessively soft yen could have a negative impact on people's livelihoods through higher import prices.
The comments prompted some participants to book profits on massive long positions for the Antipodean currencies. Since November, the Aussie and kiwi surged around 13 percent on expectations the Bank of Japan will be forced to take bold action to beat deflation and jump-start a sluggish economy.
The yen rebound weighed on the Antipodeans against their US counterpart.
The Aussie was contained at $1.0555, from $1.0568 early, though still within easy reach of a four-month peak just shy of $1.0600 set last week.
Support was found at $1.0502, the 38.2 percent of the $1.0345/$1.0599 move, with stops cited below. Traders said option related sellers were lined up ahead of $1.0600 with stops above $1.0625.
The kiwi eased to $0.8405, having initially risen to $0.8430 after a surprise jump in New Zealand business confidence.
"(The NZIER survey) indicates that the economy in Q4 got back on a positive track after weakness in Q3," said Imre Speizer, currency strategist at Westpac.
The NZ currency was still near a 16-month peak of $0.8477 set in December. Technical support was seen at $0.8405, roughly around its 100- and 200-hourly moving averages.
Earlier in the session, the Antipodeans had held their ground after US Fed Chief Ben Bernanke said the recovery was still fragile and warned the economy was at risk from political gridlock over the deficit.
The comments were taken as evidence the Fed would not stop its asset buying programme anytime soon, which was positive for bonds but a weight on the US dollar.
The Aussie and kiwi dollars nursed losses versus the euro. The single currency last fetched A$1.2671, after hitting an offshore high of A$1.2709, the best since Jan 2.
Against the kiwi, it rose to NZ$1.5908, not far from a two-week peak of NZ$1.5976 set on Monday.
New Zealand government bonds inched up, pushing yields as much as 4 basis points lower at the short end of the curve.
Australian government bond futures rose, with the three-year contract up 0.03 points at 97.190 and the 10-year contract 0.02 points higher at 96.585.