The external affairs ministry said this was decided due to Modi's "unavoidable domestic commitments and pre-scheduled travels within" India.
An official spokesman said that during his last visit to Kathmandu, Modi had expressed a desire to visit other places in Nepal "to highlight the strong civilizational links and unparalleled people-to-people contacts between the two countries".
The three places he had specifically desired to go were Lumbini, the birthplace of Lord Buddha, as well as Janakpur and Muktinath, which both Hindus and Buddhists hold as sacred.
"There has been widespread interest in the prime minister's schedule in the upcoming visit to Nepal for the SAARC Summit.
"Due to (Modi's) unavoidable domestic commitments and pre-scheduled travels within the country, he will travel only to Kathmandu to attend the SAARC Summit," the spokesman said.
The government said Modi "deeply values the special relationship between India and Nepal and will always welcome every occasion to visit Nepal and interact with the leadership and the people of Nepal.
"He looks forward to an early opportunity to visit Janakpur, Lumbini, Muktinath and other places in Nepal."