Mnangagwa addressed Zimbabweans on Tuesday calling for unity and patriotism to work towards rebuilding the country's battered economy.
The protests, which have the backing of the main opposition MDC Alliance, were called to show anger at government corruption but a number of the organisers were in hiding.
The three were abducted and tortured in May, but the government claims the three faked their disappearance and arrested them.
Their alleged abduction and torture in May shocked the international community and sparked criticism of the Zimbabwe government.
The experts, who included members of the UN’s working group on enforced disappearances, said last year alone 49 cases of abduction and torture were reported in the country.
The meeting took place at Mnangagwa's farm in central Zimbabwe on Sunday, fuelling criticism that negotiations are one-sided.
On Monday, anti-riot police stormed the premises forcing staff to leave.
The police said they discovered more than 200 anti-riot police helmets stashed in the basement of a nearby building.
On Tuesday, MDC leader Nelson Chamisa said it was un-African for some to celebrate while others were mourning.
Chibaya is facing charges after he failed to stop a protest two weeks ago.
The MDC, which accuses President Emmerson Mnangagwa’s government of repression and economic mismanagement, called a demonstration last Friday as the start of a nationwide protest movement but it was banned by the police.
The embassies of the European Union, United Kingdom, France, the United States and Canada issued a joint statement on Tuesday criticising President Emmerson Mnangagwa's government for cracking down on recent MDC-led protests.
The EU, together with the US, Britain and other Western nations, said the recent harassment and intimidation of rights defenders was a cause for great concern.
There were no reports that opposition supporters tried to defy the ban, nor were there reports of a police crackdown on protesters as there were on Friday in Harare.
Soldiers and armed police on horseback and in trucks patrolled the central business district and most of the high-density suburbs.
Zimbabwe’s capital, Harare, was on lockdown on Friday as riot police clashed with citizens and protesters of the Movement for Democratic Change in the city's CBD.
The southern African nation is enduring shortages of foreign currency, fuel and bread as well as 18-hour power cuts. The power outages threaten mining and industrial output and have upended lives.
Job Sikhala was summoned to report to police in Harare on Tuesday after he reportedly made the call at the weekend.
