Hachala Hundessa became a symbol of the Oromo struggle during years of anti-government protests that swept Abiy to power in 2018.
His shooting death last week sparked days of protests and ethnic violence that killed 239 people, according to police figures.
"The assassination was intended to be a cover to take power from the incumbent by force," attorney general Abebech Abbebe said in a statement Friday aired on state television, without providing details.
Though Abiy is Ethiopia's first Oromo head of state, Oromo nationalists accuse him of insufficiently championing their interests since taking office, a complaint echoed by many protesters last week.
Abebech said that along with the two men who have allegedly confessed to the crime, the government has identified a third suspect who remains on the run.
One of the men in custody identified the masterminds of the alleged plot as members of a rebel group the government believes is affiliated with the opposition Oromo Liberation Front (OLF) political party, Abebech said.
The OLF, a former rebel movement, returned to Ethiopia from exile after Abiy took office and has repeatedly disavowed any links to armed insurgents.
The internet remained shut off Friday for an 11th consecutive day, though Addis Ababa remains calm and Abiy's office issued a statement saying the surrounding Oromia region had "returned to calm and citizens have resumed normal activities".
In her statement, however, Abebech said unnamed agitators were calling for additional protests and road blockages in the coming days.
"There are those that have hidden themselves in nice places but are calling on Ethiopian youth to fight each other, close roads and to cease working as part of a rebellion call," Abebech said.
"Above all we call on our people to disobey this rebellion call and to thwart it."