"He has obtained political asylum following a March 30 decision" to that effect, Charlie Mingiedi said.
"It is a relief. He can now once again involve himself in political life," Mingiedi said of the controversial Mukungubila, who claims to be a prophet.
South African officials, who had previously rejected the pastor's asylum requests, made no immediate comment on the said approval.
Kinshasa wants to question Mukungubila, who has described himself as God's "last envoy to humanity", over violence which left more than 100 dead.
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He fled to South Africa, where he was arrested in May 2014 on an Interpol warrant issued at Kinshasa's behest at his house in the suburbs of Johannesburg before being released on bail.
At the time his lawyer said he stood accused of murder, intentional and aggravated assault, malicious destruction, as well as illegal and arbitrary detention.
South African authorities eventually dropped the case, citing lack of evidence.
Mukungubila, who denies the allegations against him, stood against President Joseph Kabila, whose regime he has bitterly criticised, in 2006 elections.
"There is no return to RDC but he will continue to mobilise the Congolese people against the dictatorship ruling the country," his spokesman said.