The opposition Movement for Democratic Change (MDC) has said that Shiri and other commanders waged a violent crackdown against MDC supporters in June, during an election campaign.
"I think the allegations are ridiculous ... there is no evidence of any training of any foreign person in Botswana"
Phandu Skelemani, Botswana's foreign minister
Morgan Tsvangirai, the leader of the MDC, subsequently boycotted the poll, clearing the way for Mugabe, the leader of Zanu-PF, to extend his 28-year rule as president.
Shiri was shot while he travelled to his farm, which was taken from a white farmer in 2000 during a campaign condemned by Britain and the United States.
The Zimbabwean government has in the past accused neighbouring Botswana of training fighters aiming to unseat Mugabe.
Both Botswana and the MDC have denied the accusation that fighters opposed to Zanu-PF are being trained there.
"I think the allegations are ridiculous ... there is no evidence of any training of any foreign person in Botswana," Phandu Skelemani, Botswana's foreign minister, told Al Jazeera.
"That is why we even invited [the Zimbabwean government] together with the troika of Swaziland, Mozambique and Angola to come and show us where the [alleged] bases are."
Shiri has been accused of leading a violent campaign against the opposition in Zimbabwe’s Matabeleland and Midlands provinces in the 1980s, in which an estimated 10,000 people died.
MDC members seized
The MDC has said in a statement that Zanu-PF loyalists had abducted 20 of its members since the attack on Shiri.
The opposition group accused Zanu-PF of using violence against MDC members and of trying to pin the blame for the attack on Shiri on its activists.
"Instead of carrying out proper investigations resulting in the shooting of Shiri, the regime, which has been hard hit by internal haemorrhage in the party's top hierarchy, is coming up with false allegations that the MDC is training its members in banditry activities in neighbouring Botswana," the MDC said.
Mugabe is facing increasing pressure to step down in the face of the country’s cholera epidemic, while regional countries are losing patience with Zimbabwe's political leaders over the failure to implement a recent power-sharing deal.
"We are concerned that they are taking longer to finalise the agreement while the humanitarian situation is deteriorating," Jacob Zuma, the leader of South Africa's ruling African National Congress, said on Tuesday.
"We have a responsibility to push them all in the right direction, and will continue to do so."