A parliamentary statement carried by the state-run Petra news agency on Wednesday, said: "This decision is unrealistic and a clear injustice.
"The Muslim Brotherhood in Jordan is a respectable charity organisation that is far removed from any terrorist activity and is an undivided part of the Jordanian national fabric.
"We call on Russia to reconsider its decision and cancel it as well as to strive to bolster relations with the Arab and Muslim worlds."
The Muslim Brotherhood was founded in Egypt in the late 1920s and has since become a worldwide Islamist movement boasting two million members and the support of three million more people around the globe.
North Caucasus groups
The Jordanian branch was set up in 1942 and plays a key role in the country's politics, having its own political party, the Islamic Action Front, which yields 17 deputies in the 110-seat parliament.
Russia's supreme court declared 17 groups, including the Muslim Brotherhood, al-Qaeda and Afghanistan's Taliban, "terrorist organisations", Russia's government daily Rossiiskaya reported on July 28.
The list included several local organisations linked to separatist and religious movements in the North Caucasus and the former Soviet republics of Central Asia.
But it did not include the Palestinian resistance group Hamas or Lebanese Shia militia Hezbollah (Party of God), both of which are considered "terrorist" organisations by the US.
"The 17 organisations on this list have been declared terrorist ... and their activities are banned on Russian territory," Yury Sapunov, head of anti-terrorism with Russia's FSB security service was quoted in the daily as saying.