Three Hindu groups backing Mr Vajpayee's party have staged protests and burned an effigy of the Pope in the weeks leading up to his 62-hour visit, his second to India. They claim conversions to Christianity are forced, and want an apology for the killings of Indians by Portuguese Catholic colonialists during the 16th-century Inquisition.
Security for the visit has been tight. Police arrested three demonstrators at the Gandhi memorial in New Delhi after they briefly waved black flags and shouted: "Stop conversions."
Visiting the memorial later, the Pope quoted Gandhi himself in the visitors' book, writing: "A culture cannot survive if it attempts to be exclusive."
At Hyderabad House, the Prime Minister's residence, John Paul also met President KR Narayanan and the opposition leader Sonia Gandhi.
The 79-year-old Pope's visit to India marks the close of a synod of Asian bishops, and also coincides today with Diwali, the Hindu festival of light.
There were fears that a document due to be released by the synod, calling for more evangelisation in Asia, might fuel Hindu opposition.
India, where Christians account for only just over 2 per cent of a population of roughly one billion, has seen a surge in anti-Christian violence over the past two years with attacks on clergy and the burning of Church property.