Emperor Akihito and Empress Michiko will meet the Indian premier and other dignitaries during their six-day visit, the first by any Japanese emperor to India.
The royal couple, who had visited India in early 1960s as crown prince and princess, were received by Prime Minister Manmohan Singh on the airport tarmac in New Delhi.
The Indian foreign ministry said the government was according "utmost importance" to the visit to ensure the royal couple have a memorable trip.
The visit "is a symbol of the goodwill of the emperor and the Japanese people towards India", a top Indian foreign ministry official told reporters in New Delhi ahead of their arrival.
"We are very honoured to be able to accept this goodwill gesture from the Japanese side," East Asia affairs director Shambhu Kumaran said.
Japan's emperor is the nominal head of state and does not enjoy political powers. But customarily, the emperor's visit to any country is highly significant and signals a high point in ties.
Japan has said the visit reflected the "very strong" relationship the two countries have forged in the last few years.
"The visit is a recognition of the very robust relationship and long historical ties between Japan and India," a Japanese embassy official said earlier this week.
The couple will take part in a host of official programmes and private engagements in Delhi before flying to the southern city of Chennai on Wednesday.
Ties between the two countries are on the upswing with Singh visiting Japan in May during which both sides agreed to enhance bilateral cooperation.
Before embarking on the India tour, the couple said they hoped their visit would contribute to deepening the friendship between the two countries.
Japan has warm commercial ties with India which is an attractive market due to its growing middle class, although its activities in South Asia are only a fraction of its investment in China.
Tokyo is also keen to forge regional partnerships to offset Beijing's growing might.