Forces set up unilaterally by some states have sparked controversy, particularly during the brutal Tigray war, with security officials operating in Amhara region accused of severe human rights abuses.
"Special forces members in the entirety of Ethiopia will be reorganised with their choices fully guaranteed and their desires respected," federal government spokeswoman Selamawit Kassa told a press conference on Friday.
She said members could either join the federal military, the regional police or return to civilian life.
Her comments followed the release of a statement by the government communications service on Thursday, announcing the start of "practical activity to enter the regions' security forces into various security structures."
Ethiopia's constitution allows its 11 states, drawn up along linguistic and cultural lines, to operate their own regional police forces.
But over the last 15 years, some states have gradually established their own forces, acting outside these constitutional constraints.
In Amhara, which neighbours Tigray, forces of this kind as well as local militias bolstered support for federal forces in their two-year war against Tigrayan rebels, until a peace deal was signed in November 2022.
On Thursday, the government said it intended "to build a strong centralised army that can maintain Ethiopia's sovereignty and unity."
"An understanding has been reached with the special forces leadership and members," it added.
The statement followed reports of localised unrest in Amhara where regional forces have begun to disarm, with Selamawit on Friday blaming the spread of "false information".
"In some places based on lack of information and also without properly understanding the programme's aims... some (problems) have occurred," she said.
"The society shouldn't listen to false information... intended to confuse the population and to create a country which has a weak and disintegrated force."
The peace deal signed last November between the Tigray People's Liberation Front (TPLF) and Ethiopia's government has sparked anger among some Amhara residents, who have a long history of border disputes with Tigray.
Since the war erupted, Amhara forces and local militias known as Fano have occupied western Tigray, an area claimed by Amhara and Tigray, which remains inaccessible to journalists.
Following a visit to Ethiopia last month, US Secretary of State Antony Blinken said Amhara forces had committed "ethnic cleansing" by forcibly transferring people out of western Tigray.
All parties to the conflict have been accused of possible war crimes by UN investigators.
The war began in November 2020 when Prime Minister Abiy Ahmed sent troops into Tigray after accusing the TPLF, once the dominant party in Ethiopia, of attacking army bases.
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