In a filmed statement distributed by government opponents, Klara Kabilova said she resigned under pressure from the president's son, Maksim Bakiev, to disrupt the opposition's campaign for October 5 local elections.
"If Maksim Bakiev wanted to intimidate me, he achieved his goal," Kabilova said. "If he wanted to offend me, he managed to."
Officials have dismissed the allegations and in turn have accused Kabilova of "irresponsible actions."
Opposition politicians have linked Kabilova's dispute with the government with her call for the release of an opposition election candidate held by police on corruption charges.
Government critics claim Kyrgyz President Kurmanbek Bakiev is attempting to manipulate the October vote to install members of his Ak Zhol party in local governments.