In early March, the government gave its consent to the formation of the splinter Brotherhood group, led by a former head of the movement.
The offshoot aims to severe ties with the Brotherhood's arm in Egypt, where hundreds of supporters have been killed and thousands detained since Islamist president Mohamed Morsi was ousted by the army in 2013.
Analysts say Jordan's recognition of the new group -- known as the Muslim Brotherhood Association -- risks fanning discontent among the traditional opposition power base at a time when the kingdom is battling jihadists in neighbouring Iraq and Syria.
"The authorities have given themselves a real dilemma by focusing on a small group without political weight or popularity," said political analyst Mohamed Abu Romman.
Jordan joined the US-led coalition fighting the Islamic State group in Iraq and Syria last year and enjoyed a groundswell of public support for air raids on the jihadists after one of its captured pilots was burned alive in January.
Amman has already arrested and imprisoned dozens of would-be fighters trying to enter Syria and there are fears that its foreign air wars could lead to blowback at home.
Abu Romman warned that Jordan's acceptance of a new Brotherhood group risked the "radicalisation" of existing Islamist outfits.
The political arm of Jordan's Muslim Brotherhood, the Islamic Action Front, has long been tolerated by authorities in Amman and makes up the strongest opposition group in parliament.
But the group accuses the government of seeking to sow discord among Brotherhood supporters by adopting a deliberately murky legal approach to its activities.
"It seems to me that their intentions aren't good," Brotherhood spokesman Badi al-Rafaia told AFP. "We only hope that the state isn't seeking a confrontation."
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RALLY CALLED OFF
A recent rally planned as a show of force for the original Jordanian Brotherhood branch had to be cancelled at the last minute after organisers were told the authorities were not authorising the gathering because of objections from the rival wing.
The Brotherhood issued a statement expressing its regret at "government measures aimed at erecting obstacles" and accused unnamed parties of "pushing the country towards a crisis".
The government denied that its recognition of the splinter group was aimed at undermining the country's historic branch.
"We are talking about the Muslim Brotherhood Association being authorised by law, and a group of citizens engaged in activities on its behalf. That is what the law says," said government spokesman Mohamed al-Momani.
Yet analysts question the wisdom of appearing to undermine Jordan's largest Islamist group as it continues its role in international military operations in Iraq and Syria and has joined a Saudi-led coalition bombing rebels in Yemen.
"The government would be making a grave error if it used its security, judicial and administrative tools to favour one group over the other," said Oreib al-Rentawi, director general of the Al-Quds Centre for Political Studies.
"The state has no interest in entering into a confrontation with the Brotherhood right now."
Jordan's acceptance of the new group contrasts markedly with recent harsher measures against the Brotherhood.
Second-in-command Zaki Bani Rsheid was sentenced in February to 18 months in jail for criticising a decision by the United Arab Emirates to outlaw the Brotherhood.
Analyst Karim Kamhawi said the government could seek to follow the lead of Egypt, the UAE and Saudi Arabia in criminalising the group.
"But politically this would be a big mistake," he said. "The fight between the Brotherhood and the state is a fight for democracy. The state needs to keep out of party political life."