The news agency reported earlier on Saturday that Jordanian security forces had arrested a former adviser to King Abdullah and others on "security related" grounds.
The army denied Saturday that Prince Hamzah, who holds no official position, had been detained.
Petra had earlier reported that two senior officials who formerly worked for the palace, along with other suspects, had been arrested for "security reasons", without providing further details. The military chief said it was being conducted in line with the law and results would be presented with full transparency.
The news comes as a shock in the desert kingdom, a close regional ally of the USA often lauded for its stability in a crisis-ridden neighborhood.
Abdullah stripped his half-brother Hamzah of his title as crown prince in 2004, saying he had made a decision to "free" him from the "constraints of the position" in order to allow him to take on other responsibilities.
Abdullah has ruled Jordan since the 1999 death of of his father, King Hussein, who ruled the country for close to half a century.
"Communication was lost with them more than three hours ago", she tweeted. General Mahmoud Yousef Huneiti issued a statement saying Prince Hamzah had not been detained but instead was "asked to stop movements and activities that were being employed to target Jordan's security and stability", adding that this was done within "the framework of comprehensive joint investigations undertaken by the security services".
He said his security detail was removed, and his phone and Internet service had been cut.
The official news agency Petra named Bassem Awadallah, chief of the royal court in 2007-2008, and Sherif Hassan bin Zaid as among an unspecified number of suspects arrested on Saturday.
I pray that all Jordanians will remember that I have always to tried to serve them to the best of my ability with what limited resources I have had, that I always will, and that God willing the situation will improve if we are able to come together and make our voice heard. Both Bahrain and the Palestinian Authority followed suit, and Egypt said that Jordan's stability is integral for Egyptian and Arab national security.
"We are closely following the reports and in touch with Jordanian officials", State Department spokesman Ned Price said. "King Abdullah is a key partner of the U.S., and he has our full support", he said.
Abdullah had appointed Hamzah crown prince in 1999 in line with Hussein's dying wish, but in 2004 stripped him of the title and gave it to his own eldest son Hussein. The king has cultivated close relations with USA and other Western leaders over the years, and Jordan was a key ally in the war against the Islamic State group. He has good relations officially with Abdullah and is a popular figure close to tribal leaders.
"(Jordanians') well being has been put second by a ruling system that has decided that its personal interests, financial interests, that its corruption is more important than the lives and dignity and future of the ten million people who live here", he said.
Videos posted online showed a heavy police deployment in the Dabouq area near the royal palaces, while the former crown prince Hamzah bin Hussein said he was confined to his home.
The current crown prince is Abdullah's oldest son, Hussein, who is 26.
King Abdullah has succeeded in bringing political stability to the country and gaining stature as a prominent Arab leader whose message of moderation has found an echo, especially in Western forums.
Lebanese Prime Minister-designate Saad al-Hariri also voiced support for King Abdullah II, saying that Jordan's stability os the basis for the stability of the whole Arab world. He later became chief executive of Tomoh Advisory, a Dubai-based consultancy.
A country of 10 million people, Jordan's economy was already suffering before the Covid pandemic hit.