The ministry said Sunday it took the incident extremely seriously and had also summoned Jordan's acting ambassador to Israel to convey its objection.
A photo published on the Jordanian website Jfranews showed Information Minister Jumana Ghuneimat stepping on a large image of the Israeli flag. Footprints were also printed on the flag, which Israel said was displayed at a gathering of Jordan's engineering union.
Israel and Jordan signed a peace agreement in 1994, but relations have often been frosty amid differences over Israeli policies in Jerusalem, where Jordan is custodian over Muslim sites, and toward the Palestinians.
Last October, Jordan's King Abdullah announced that he intends to cancel the appendices to the peace treaty with Israel, reclaiming Jordanian sovereignty over some territories in the Arava region and the surrounding agricultural areas near Naharayim.
The appendices to the peace agreement concern mainly the lease of the Island of Peace in Naharayim and the Tzofar enclave in the Arava, leased by Israel since the signing of the peace treaty between the two countries nearly 25 years ago.