The Israeli Foreign Ministry on Sunday summoned acting Jordanian Ambassador Mohammed Hmaid for a reprimand after local media published a photo of a Jordanian minister stepping on an image of the Israeli flag.
In parallel, the Israeli Embassy in Amman delivered an official strong condemnation of the incident to the kingdom's government, the ministry said.
The photo, published on the Jordanian website Jfranews, showed Information Minister Jumana Ghuneimat walking over an Israeli flag painted on the floor of the headquarters of Jordan's professional unions in Amman.
Footprints were also painted on the flag.
Israel and Jordan signed a peace agreement in 1994, but relations have often been frosty, with differences over Israeli policies in Jerusalem, where Jordan is custodian over Muslim sites, and toward the Palestinians.
The unions are controlled by Jordan's mainly Islamist opposition, known for its fierce ideological objection to the peace treaty between the two nations or any other move toward normalizing ties with the Jewish state.
The incident occurred last Thursday at Jordan's Trade Union building, when Ghuneimat was on her way to a meeting between Jordanian Prime Minister Omar al-Razzaz and union representatives.
Razzaz entered the building through a rear door, avoiding having to walk over the flag.
Majed Qatarneh, a spokesman for Jordan's Foreign Ministry, confirmed that Israel had sought clarifications over the incident, saying the ministry was handling the issue through "diplomatic channels."
"The Israeli side was informed that the building is a private one and the minister entered it from the main entrance for an official meeting," he said. "We have emphasized that we respect the peace treaty with Israel."