Fadnavis, who himself is grappled with a simmering farmers' protest in his state for quite some time now, said there could be no justification for such killings.
"What happened in Madhya Pradesh is unfortunate (and) no government ever wants to do that. But the situation also was very grave, it could have turned more problematic," he told reporters here in response to a query on farmers' stir in Madhya Pradesh.
However, Fadnavis hailed the steps taken by MP Chief Minister Shivraj Singh Chouhan to improve farm production in his state during his over a decade-long rule.
Fadnavis is in Kerala to participate in events organised by the state unit of the BJP to mark the Narendra Modi government's three years at the Centre.
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Admitting that there were issues in the farm sector in Maharashtra, the Chief Minister said it happened because the farm prices are no more controlled by government post globalisation.
"We in Maharashtra had successive drought for four years. And due to those droughts, yes, there is a distress amongst farmers," Fadnavis said.
He said the farm crisis which was there is not pan Maharashtra.
"It was in certain parts of Maharashtra and the life was not affected even a single day. But still we feel that demands of farmers are there. We are trying to address it," he said.
The Chief Minister said people of the state knew that his government was working with good intentions and that helped the BJP to sweep the elections held to local bodies in the state recently.
Fadnavis also hit out at Kerala Chief Minister Pinarayi Vijayan over alleged political killings in the state.
He said Vijayan should concentrate on issues of governance rather than convening meetings of chief ministers on the Centre's notification banning sale and purchase of cattle for slaughter in animal market.
"The more grave situation here is political killings. I think he should concentrate more on that. Whether these killings are state sponsored is something which I think he needs to answer," he said.
"Democracy is all about discussion. We are not enemies.. We are political opponents.. Our ideologies may differ.. We may defeat each other in elections.. But when in democracy you start killing your political opponents, you start killing the ideologies because we differ in ideologies we start defeating the democracy," he said.
The confirmation that the five farmers were killed in police firing bears significance as the MP government had initially claimed that the police did not fire at the agitating farmers.
Mandsaur has been on the boil since the farmers' agitation in the district turned violent.
Farmers in western Madhya Pradesh are protesting since June 1 over various demands including fixing of a crop prices.
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