Military leader Capt. Amadou Sanogo overthrew President Amadou Toumani Touré following a coup on March 22.
In a new report Human Rights Watch warn the security forces of Sanogo are also responsible for a series of serious rights violations.
The watchdog has interviewed about 30 people for its report entitled: Mali: Security Forces 'Disappear' 20, Torture Others
Forced disappearance, torture
Witnesses told Human Rights Watch (HRW) Sanogo loyalists are responsible for the forcible disappearance of at least 20 soldiers linked to an April 30 counter-coup. They also tortured more than a dozen of other soldiers also linked to the rebellion, the report said.
Most of the disappeared were part of an elite unit of paratroopers known as the Red Berets. They were detained after being accused of participating in the April counter-coup.
During the insurgency the Red Berets attacked the state radio and television building, the airport in Bamako, and the Kati military camp, 15 kilometres from Mali's capital, Bamako.
Soon after bringing the situation under control, security forces started rounding up people they thought had participated or supported the coup, witnesses said.
Interviews also described how detainees at the Kati military base were tortured by the security forces, being dragged handcuffed and hogtied along the ground, beaten with batons, sticks, and gun butts, kicked in the back, head, ribs, genitals, and elsewhere. Others were stabbed in their extremities, the report adds.
Members of the security services are also leading intimidation campaigns against journalists who investigated the aftermath of the April counter-coup.
HRW report cited the case of at least five journalists who were called for questioning and pressured into revealing their sources, desisting from publishing or from speaking out about the events.
In July two journalists were also abducted by armed men and beaten up before being dropped in the outskirts of the capital and warned to stop criticising the military.
Sanogo directly involved?
Witnesses told HRW that the abuses were committed by members of the security services, including soldiers, policemen and national guardsmen who are all Sanogo loyalists.
Two witnesses even told HRW that Sanogo was present at the military base in Kati when torture or other forms of ill-treatment were taking place.
Another witness said he saw the military leader kick one of the prisoners who has since then disappeared and heard him threaten several others.
HRW also said most of the people interviewed were convinced officers who committed human rights violations reported directly to Sanogo.
There are unconfirmed reports that the men were executed and buried in the town of Diago, some 12 kilometers from Kati, the report says.
"Malian authorities have a duty to the victims of torture and the families of the disappeared to ensure these crimes are investigated and those responsible brought to book," said Daniel Bekele, Africa director at Human Rights Watch.
"Even at this chaotic and difficult time in Mali, authorities should ensure that the horrific treatment and other violations should be promptly addressed."
Sanogo and his followers plotted a coup in March after criticising the Toure government for failing to bring a rebellion by Tuaregs in Northern Mali under control.
Following international pressure Sanago agreed to hand over power to a transitional government in April but remains an influential figure.
Last week, the government of Mali, as a state party to the International Criminal Court (ICC), referred "the situation in Mali since January 2012" to the ICC prosecutor for investigation.
"The Economic Community of West African States (ECOWAS) and other governments that have voiced their concern about abuses committed in the context of the armed conflict in the North and the March coup shouldn't go silent now," Bekele said.
"Mali's partners should insist the transitional government take concrete and urgent steps to stem any further deterioration in respect for the rule of law," he added.