A top party later said action will be taken against Khadse but it will not happen "today", indicating that it may come in some time.
After a meeting with Shah, Fadnavis said he has submitted a report to him and they discussed the matter.
"I have submitted a factual report on the matters which have come up recently. We have discussed them as well. The party will direct whatever appropriation has to be taken ahead," he told reporters after the meeting.
Khadse has been attacked by political rivals and BJP ally Shiv Sena over the alleged impropriety over purchase of a land belonging to the government-owned MIDC in Pune at a throwaway price.
BJP sources said Shah considers allegations against Khadse "serious". Political rivals are also using them to put the party in the dock over its claim of providing "corruption- free" government.
Khadse is in a spot over the purchase of 3-acre Maharashtra Industrial Development Corporation land in Bhosari allegedly at a low price of around Rs 3.75 crore from its original owner in the name of his wife and son-in-law. The market value of the land is reportedly Rs 40 crore.
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Speaking to reporters in his hometown of Jalgaon, Khadse said he would abide by the party's directives.
"I will follow my party's instructions and will abide by its decisions," he told news channels.
He, however, added: "The party leadership will not arrive at any decision in my case unless it is convinced (about the facts).
"I have worked for the party for the last 40 years to build it in the state. This cannot be negated suddenly. I have documents about my transactions...(those transactions) have no discrepancy," he said.
