Khama, 70, made damning allegations in a recent interview with AFP claiming his handpicked successor Mokgweetsi Masisi had "totally undermined democracy, human rights, the rule of law."
But the government denied the "unfounded" accusations, describing them in a statement as "outrageous and unfortunate, politically motivated and with the sole intention of tarnishing the good image" of Botswana and its government.
Khama led Africa's top diamond producing nation for a decade until 2018, before handing the reigns to Masisi, who had been his deputy.
"Botswana is a democratically governed nation-state that keenly respects and observes the rule of law and ethics of good governance underpinned by adherence to a culture of human rights," said the government.
Khama, who has been based in South Africa since November 2021, drew parallels between Masisi and ex-American president Donald Trump.
"Botswana has been a democracy, right from independence, we had a very good reputation for democracy, we were a shining light on the African continent, we were renowned worldwide for our adherence to democracy and then you get this one man who comes in one day and just overturns everything," said Khama.
"And this is the Botswana version of Donald Trump in Masisi."
Government said it concluded Khama's motives coming a year before general elections due in 2024, were "questionable."
In 2018 Khama dramatically quit the long-ruling Botswana Democratic Party, which had been co-founded by his father Seretse Khama, Botswana's first president, and went on to back an opposition party.
He has vowed to bring the opposition parties into an electoral alliance to remove Masisi through the ballot box in next year's polls.
The former senior military officer and head of state said he had intelligence information on plans to arrest and poison him if he returned home.
Gaborone rubbished the claim.
"A democratic social order continues to manifest in Botswana, and there is no threat by the state on Dr. Khama's life," it said.
Independent organizations "continuously" rank Botswana high on good governance indices, it noted, citing a 2023 USAID report which placed the country third out of 49 African states for corruption control.