"Rest in Peace President Shimon Peres, a Man of War and a Man of the still elusive Peace in the Middle East," Sheikh Khaled bin Ahmed al-Khalifa said on Twitter.
The response to his tweet was swift.
Like most Arab countries, Bahrain does not have diplomatic relations with Israel, and many Arabs associate Peres with the successive wars that have rocked the Middle East rather than the Oslo accords with the Palestinians that earned him the Nobel Peace Prize.
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"The foreign minister is paying tribute and praying for the Zionist terrorist and the killer of children," complained former opposition lawmaker Jalal Fairooz.
Another critic, Khalil Buhazaa, tweeted: "Diplomacy does not mean rudeness."
Peres died on Wednesday aged 93 after suffering a major stroke.
He won the 1994 Nobel Peace Prize jointly with prime minister Yitzhak Rabin and Palestinian leader Yasser Arafat for his role in negotiating the Oslo accords, which envisioned an independent Palestinian state.
But he is also remembered in the Arab world as the man who ordered the devastating "Grapes of Wrath" operation against Lebanon in 1996, which left 175 people dead, most of them civilians.