He said Modi's statement on the issue was an insult to Kashmiri people.
"When Kashmiri Pandits left the Valley, Jagmohan, who has not parted ways with BJP yet, as far as I know, was ruling the state (as Governor). Farooq Sahib was not in power.
"Jagmohan was appointed by Mufti Mohammad Sayeed (now PDP patron), who was the Home Minister in V P Singh cabinet. V P Singh was heading the government with BJP support.... I hope they (BJP leaders) remember this," he told reporters.
Hitting back at Farooq Abdullah for his remarks that those who vote for Modi should drown in sea, Modi today said the policies of Sheikh Abdullah, Farooq and his son Omar were responsible for communalising the state politics and for Kashmiri Pandits being driven out on the basis of religion.
"Majority of Kashmiri Muslims are pained at the exodus of Kashmiri Pandits and want them to come back. Modi has insulted the people of Kashmir by his statement," Omar said.
He said people of Kashmir do not need a lesson on secularism from BJP or Modi.
"People of Kashmir gave a living example of secularism in 1947 when Muslims and Hindus were killing each other. I feel it is weird that Modi is giving a lecture on secularism to people of Kashmir," he added.
He said Amarnath Yatra, about which the BJP leaders often make noises, is facilitated by Kashmiri Muslims. Omar said Modi had a problem of "distorting history to suit his own ends".'
Omar asked why Modi did not campaign in the Valley.
"Modi sahib, you do not have the courage to come to Kashmir to seek votes. You have set out to become the Prime Minister of the country but you will not come to Kashmir for seeking votes.
"You will go to Jammu and Ladakh but not the Valley because the ideas you have for this place, the way you have tried to defame people, I don't think you will have any place in their hearts," Omar told reporters here.
Omar said the three BJP candidates in the Valley must be feeling orphaned as no senior leader turned up to campaign for them.
Asked if he was throwing a challenge to Modi, Omar said the last time he dared the BJP leader for a debate on Article 370, he chose to shy away.
"I was told I am not of his stature. So who am I to challenge him! I am just stating a fact," he said.
Omar said he does not need a certification for secular credentials from either BJP or Modi and would prefer to quit politics, if it came to that.
"We don't need a certificate of being secular from Modi or the BJP. If it comes to the point that they have to issue a certificate, I will have to quit politics," he said.
Later, Omar wrote on twitter.com: "Modi forgets that Sheikh Abdullah chose a secular India rather than Muslim Pakistan and then spent two decades incarcerated but didn't waver."
The Chief Minister said BJP was only using the pain of Kashmiri pandits for political mileage and Modi's speech at a poll rally in Jammu region was evidence of that.
"Modi remembered every community in his speech but forgot the Kashmiri Pandits. You have to see what the BJP MLAs did when the (Hindu Temples and) Shrine (Protection) Bill was tabled in the state assembly early this year," he said.
Asked if he agreed with Farooq's statement, Omar said it was said in the context of a BJP leader telling opponents of the BJP Prime Ministerial candidate to go to Pakistan. "It is for the Election Commission to take a decision on it," he said.