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During his visits to Rajghat and Sadaiv Atal, the party sources said, he will be accompanied by all the 303 newly-elected BJP Members of Parliament to pay homage to Gandhi and Vajpayee.
The prime minister visited Rajghat, the memorial of Mahatma Gandhi, around 7 am.
Later, he went to Sadaiv Atal, the lotus-shaped memorial of former prime minister Vajpayee.
Several senior BJP leaders, including party chief Amit Shah, were also present.
Later, in a series of tweets, Modi said, "This year, we mark the 150th Jayanti of Bapu. May this special occasion further popularise Bapu's noble ideals and continue inspiring us to empower the lives of the poor, downtrodden and marginalised."
Modi said Vajpayee would have been very happy to see the BJP get such a great opportunity to serve people.
"Motivated by Atal Ji's life and work, we will strive to enhance good governance and transform lives," the PM said.
Referring to his visit to the war memorial, he said, India is proud of all those brave men and women martyred in the line of duty.
"Our government will leave no stone unturned to safeguard India's unity and integrity. National security is our priority," he tweeted.
Modi and his council of ministers will take oath at 7 pm Thursday at the Rashtrapati Bhavan.
Top opposition leaders including Congress President Rahul Gandhi and UPA Chairperson Sonia Gandhi, corporate honchos, film stars, chief ministers and a galaxy of leaders from BIMSTEC countries will be on hand to watch President Ram Nath Kovind administer the oath of office and secrecy to 68-year-old Modi and his ministerial colleagues at the forecourt of majestic Rashtrapati Bhavan.
Meanwhile, the security has tightened up in the national capital with the deployment of around 10,000 security personnel from Delhi Police and paramilitary forces as nearly 8,000 guests are expected to attend the biggest-ever event held in the historic premises.
The oath taking ceremony will be followed by the dinner. The Prime Minister will attend the dinner, along with some officials. With the swearing-in scheduled for 7 p.m., dinner will be light as it will be served a little late in the evening.
The dinner will have both vegetarian and non-vegetarian options and include soup, fish, chicken, vegetables and the "Dal Raisina" - a variant of popular 'maa ki dal'.