The Nikkei ended 0.5 percent lower to 21,687.10, after rising for the past two days. The market, along with a host of global risk assets, had a solid session on Tuesday after China's President Xi Jinping helped ease fears over a US-China trade war.
Investors were keeping a wary eye on discussions between US President Donald Trump and Western allies on possible military action over a suspected poison gas attack on Saturday in Syria, allegedly ordered by President Bashar al-Assad.
Retail stocks lost ground after department store operator J.Front Retailing dived 9.3 percent after its profit forecast for this fiscal year undershot market expectations. Rival Takashimaya Co tumbled 3.3 percent.
Food shares also lost ground, with Kikkoman shedding 3.6 percent and Asahi Group sliding 2.2 percent.
SoftBank Corp, Sprint Corp's majority owner, surged 3.5 percent after sources said that Sprint has restarted talks to merge with T-Mobile US Inc.
SoftBank contributed a hefty 29 points to the Nikkei index.
The broader Topix declined 0.4 percent to 1,725.30.